[ { "id": "O95714-1.4029.4029", "start_pos": 4029, "end_pos": 4029, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TGYGAGGRLGIGGTESVSTP", "down_seq": "LLESIQHVFIKKVAVNSGGK", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "28135623", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T4029", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O95714-1.4022.4022", "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": "O95714-1.4077.4077", "start_pos": 4077, "end_pos": 4077, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGEVYSWGEAEDGKLGHGNR", "down_seq": "PCDRPRVIESLRGIEVVDVA", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [ "n-glyco-sequon-loss", "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: n-glyco-sequon-loss (NRS->NRI).", "chr_id": "15", "chr_pos": "28135478", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S4077", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O95714-1.4075.4075", "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": "O95714-1.4183.4183", "start_pos": 4183, "end_pos": 4183, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759263561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759263561", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759263561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759263561", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759263561", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759263561", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DDTVWSWGDGDYGKLGRGGS", "down_seq": "GCKVPMKIDSLTGLGVVKVE", "snv": [ { "evidence": [ { "id": "rs759263561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759263561" }, { "id": "rs759263561", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759263561" }, { "id": "rs759263561", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759263561" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DGC->NGC).", "chr_id": "15", "chr_pos": "28132123", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D4183", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O95714-1.4182.4182", "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": "O95714-1.4213.4213", "start_pos": 4213, "end_pos": 4213, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1889999019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1889999019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1889999019", "url": "https://www.ensembl.org/id/rs1889999019", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SLTGLGVVKVECGSQFSVAL", "down_seq": "KSGAVYTWGKGDYHRLGHGS", "snv": [ { "evidence": [ { "id": "rs1889999019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1889999019" }, { "id": "rs1889999019", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1889999019" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TKS->NKS).", "chr_id": "15", "chr_pos": "28130527", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T4213", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4238.4238", "start_pos": 4238, "end_pos": 4238, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VYTWGKGDYHRLGHGSDDHV", "down_seq": "RPRQVQGLQGKKVIAIATGS", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "28130253", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R4238", "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:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4283.4283", "start_pos": 4283, "end_pos": 4283, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776669434", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776669434", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776669434", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776669434", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776669434", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776669434#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776669434", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776669434", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "CCTEDGEVYTWGDNDEGQLG", "down_seq": "GTTNAIQRPRLVAALQGKKV", "snv": [ { "evidence": [ { "id": "rs776669434", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776669434" }, { "id": "rs776669434", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776669434" }, { "id": "rs776669434", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776669434#frequency_tab" }, { "id": "rs776669434", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776669434" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DGT->NGT).", "chr_id": "15", "chr_pos": "28125149", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D4283", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4355.4355", "start_pos": 4355, "end_pos": 4355, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "YNHLQEIPIIALRNRLLLLH", "down_seq": "LSELFCPCIPMFDLEGSLDE", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HLS->NLS).", "chr_id": "15", "chr_pos": "28124162", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H4355", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "O95714-1.4372.4372", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O95714-1.4374.4374", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4372.4372", "start_pos": 4372, "end_pos": 4372, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLHHLSELFCPCIPMFDLEG", "down_seq": "LDETGLGPSVGFDTLRGILI", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "28124110", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S4372", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O95714-1.4355.4355", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95714-1.4374.4374", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4374.4374", "start_pos": 4374, "end_pos": 4374, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1424541635", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1424541635", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1424541635", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1424541635", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HHLSELFCPCIPMFDLEGSL", "down_seq": "ETGLGPSVGFDTLRGILISQ", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" }, { "id": "rs1424541635", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1424541635" }, { "id": "rs1424541635", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1424541635" } ], "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 (DET->NET).", "chr_id": "15", "chr_pos": "28124105", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D4374", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O95714-1.4355.4355", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95714-1.4372.4372", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4401.4401", "start_pos": 4401, "end_pos": 4401, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SVGFDTLRGILISQGKEAAF", "down_seq": "KVVQATMVRDRQHGPVVELN", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "3", "frequency": "0.4", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "15", "chr_pos": "28121417", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R4401", "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: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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "O95714-1.4410.4410", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4410.4410", "start_pos": 4410, "end_pos": 4410, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ILISQGKEAAFRKVVQATMV", "down_seq": "DRQHGPVVELNRIQVKRSRS", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "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": "15", "chr_pos": "28121390", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R4410", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O95714-1.4401.4401", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4438.4438", "start_pos": 4438, "end_pos": 4438, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs953713630", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs953713630", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs953713630", "url": "https://www.ensembl.org/id/rs953713630", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VELNRIQVKRSRSKGGLAGP", "down_seq": "GTKSVFGQMCAKMSSFGPDS", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" }, { "id": "rs953713630", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs953713630" }, { "id": "rs953713630", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs953713630" } ], "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 (DGT->NGT).", "chr_id": "15", "chr_pos": "28117115", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D4438", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4476.4476", "start_pos": 4476, "end_pos": 4476, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PDSLLLPHRVWKVKFVGESV", "down_seq": "DCGGGYSESIAEICEELQNG", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DDC->NDC).", "chr_id": "15", "chr_pos": "28116848", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D4476", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4650.4650", "start_pos": 4650, "end_pos": 4650, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YVRLAINYRLHEFDEQVAAV", "down_seq": "EGMARVVPVPLLSLFTGYEL", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "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 (4).", "chr_id": "15", "chr_pos": "28113644", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R4650", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4716.4716", "start_pos": 4716, "end_pos": 4716, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PSASLIQWFWEVMESFSNTE", "down_seq": "SLFLRFVWGRTRLPRTIADF", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "28113157", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R4716", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O95714-1.4710.4710", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O95714-1.4726.4726", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.471.471", "start_pos": 471, "end_pos": 471, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs768897624", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768897624", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768897624", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768897624", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768897624", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768897624#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768897624", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768897624", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LGVTQIACAEKRFLILSRNG", "down_seq": "VYTQAYNSDTLAPQLVQGLA", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" }, { "id": "rs768897624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768897624" }, { "id": "rs768897624", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768897624" }, { "id": "rs768897624", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768897624#frequency_tab" }, { "id": "rs768897624", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768897624" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGC).", "chr_id": "15", "chr_pos": "28269283", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R471", "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:0081203", "recommended_name": { "id": "DOID:0081203", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0081203", "name": "autosomal recessive intellectual developmental disorder 38", "description": "An autosomal recessive intellectual developmental disorder that has_material_basis_in homozygous mutation in the HERC2 gene on chromosome 15q13." }, "synonyms": [ { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "developmental delay with autism spectrum disorder and gait instability", "description": "Developmental delay with autism spectrum disorder and gait instability is a rare, genetic, neurological disorder characterized by infant hypotonia and feeding difficulties, global development delay, mild to moderated intellectual disability, delayed independent ambulation, broad-based gait with arms upheld and flexed at the elbow with brisk walking or running, and limited language skills. Behavior patterns are highly variable and range from sociable and affectionate to autistic behavior." }, { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "developmental delay with ASD and gait instability", "description": "" }, { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "intellectual developmental disorder, autosomal recessive 38", "description": "" }, { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "intellectual disability, autosomal recessive type 38", "description": "" }, { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "mental retardation, autosomal recessive type 38", "description": "" }, { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "MRT38", "description": "" }, { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "intellectual disability, autosomal recessive 38", "description": "" }, { "id": "MONDO:0014224", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014224", "name": "mental retardation, autosomal recessive 38", "description": "" }, { "id": "MIM:615516", "resource": "MIM", "url": "https://www.omim.org/entry/615516", "name": "Intellectual developmental disorder, autosomal recessive 38", "description": "Intellectual developmental disorder, autosomal recessive 38" } ], "unlinked_id_list": [], "evidence": [ { "id": "615516", "database": "MIM", "url": "https://www.omim.org/entry/615516" }, { "id": "0081203", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0081203" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4726.4726", "start_pos": 4726, "end_pos": 4726, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EVMESFSNTERSLFLRFVWG", "down_seq": "TRLPRTIADFRGRDFVIQVL", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "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": "15", "chr_pos": "28113126", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R4726", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O95714-1.4710.4710", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O95714-1.4716.4716", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4769.4769", "start_pos": 4769, "end_pos": 4769, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YNPPDHFLPESYTCFFLLKL", "down_seq": "RYSCKQVLEEKLKYAIHFCK", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "28111963", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P4769", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.4808.4808", "start_pos": 4808, "end_pos": 4808, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs188787231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188787231", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs188787231", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188787231", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs188787231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188787231", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs188787231", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188787231#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs188787231", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188787231", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "CKSIDTDDYARIALTGEPAA", "down_seq": "DSSDDSDNEDVDSFASDSTQ", "snv": [ { "evidence": [ { "id": "rs188787231", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188787231" }, { "id": "rs188787231", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188787231" }, { "id": "rs188787231", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188787231" }, { "id": "rs188787231", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188787231#frequency_tab" }, { "id": "rs188787231", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188787231" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "15", "chr_pos": "28111846", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D4808", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O95714-1.4809.4809", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95714-1.4810.4810", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O95714-1.4811.4811", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O95714-1.4812.4812", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O95714-1.4814.4814", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O95714-1.4827.4827", "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": "O95714-1.4809.4809", "start_pos": 4809, "end_pos": 4809, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762060698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762060698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762060698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762060698", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762060698", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762060698#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762060698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762060698", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KSIDTDDYARIALTGEPAAD", "down_seq": "SSDDSDNEDVDSFASDSTQD", "snv": [ { "evidence": [ { "id": "rs762060698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762060698" }, { "id": "rs762060698", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762060698" }, { "id": "rs762060698", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762060698#frequency_tab" }, { "id": "rs762060698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762060698" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "15", "chr_pos": "28111843", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D4809", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O95714-1.4808.4808", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O95714-1.4810.4810", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95714-1.4811.4811", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O95714-1.4812.4812", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O95714-1.4814.4814", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O95714-1.4827.4827", "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": "O95714-1.4812.4812", "start_pos": 4812, "end_pos": 4812, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1466221657", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1466221657", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1466221657", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1466221657", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DTDDYARIALTGEPAADDSS", "down_seq": "DSDNEDVDSFASDSTQDYLT", "snv": [ { "evidence": [ { "id": "rs1466221657", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1466221657" }, { "id": "rs1466221657", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1466221657" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "15", "chr_pos": "28111834", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D4812", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O95714-1.4808.4808", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O95714-1.4809.4809", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95714-1.4810.4810", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O95714-1.4811.4811", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95714-1.4814.4814", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O95714-1.4827.4827", "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": "O95714-1.543.543", "start_pos": 543, "end_pos": 543, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DGGRLGHGDTVPLEEPKVIS", "down_seq": "FSGKQAGKHVVHIACGSTYS", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "28265946", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A543", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "O95714-1.559.559", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O95714-1.561.561", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.559.559", "start_pos": 559, "end_pos": 559, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KVISAFSGKQAGKHVVHIAC", "down_seq": "STYSAAITAEGELYTWGRGN", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "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": "15", "chr_pos": "28265898", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G559", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O95714-1.543.543", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95714-1.561.561", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.561.561", "start_pos": 561, "end_pos": 561, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753784290", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753784290", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753784290", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753784290", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753784290", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753784290#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753784290", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753784290", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ISAFSGKQAGKHVVHIACGS", "down_seq": "YSAAITAEGELYTWGRGNYG", "snv": [ { "evidence": [ { "id": "rs753784290", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753784290" }, { "id": "rs753784290", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753784290" }, { "id": "rs753784290", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753784290#frequency_tab" }, { "id": "rs753784290", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753784290" } ], "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 (TYS->NYS).", "chr_id": "15", "chr_pos": "28265891", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T561", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O95714-1.543.543", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95714-1.559.559", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O95714-1.581.581", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.581.581", "start_pos": 581, "end_pos": 581, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs995605135", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs995605135", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs995605135", "url": "https://www.ncbi.nlm.nih.gov/snp/rs995605135#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs995605135", "url": "http://gnomad.broadinstitute.org/awesome?query=rs995605135", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TYSAAITAEGELYTWGRGNY", "down_seq": "RLGHGSSEDEAIPMLVAGLK", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" }, { "id": "rs995605135", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs995605135" }, { "id": "rs995605135", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs995605135#frequency_tab" }, { "id": "rs995605135", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs995605135" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NYG->NYS).", "chr_id": "15", "chr_pos": "28265832", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G581", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O95714-1.561.561", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O95714-1.594.594", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.594.594", "start_pos": 594, "end_pos": 594, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TWGRGNYGRLGHGSSEDEAI", "down_seq": "MLVAGLKGLKVIDVACGSGD", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "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 (3).", "chr_id": "15", "chr_pos": "28265707", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P594", "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: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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O95714-1.581.581", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.737.737", "start_pos": 737, "end_pos": 737, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs752780957", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752780957", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752780957", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752780957", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752780957", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752780957", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GSTHCLALTEDSEVHSWGSN", "down_seq": "QCQHFDTLRVTKPEPAALPG", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" }, { "id": "rs752780957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752780957" }, { "id": "rs752780957", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752780957" }, { "id": "rs752780957", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752780957" } ], "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 (DQC->NQC).", "chr_id": "15", "chr_pos": "28260884", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D737", "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": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.886.886", "start_pos": 886, "end_pos": 886, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KQTVVTLASSAGVLSTVQSA", "down_seq": "QAVLQSGWSVLLPTAEERAR", "snv": [ { "evidence": [ { "id": "O95714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95714" } ], "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 (4).", "chr_id": "15", "chr_pos": "28256179", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A886", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95714-1.984.984", "start_pos": 984, "end_pos": 984, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1258637047", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258637047", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1258637047", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258637047", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAQKEKEIDEQEANASTFHR", "down_seq": "RTPLDKDLINTGICESSGKQ", "snv": [ { "evidence": [ { "id": "rs1258637047", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258637047" }, { "id": "rs1258637047", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258637047" } ], "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 (SRT->NRT).", "chr_id": "15", "chr_pos": "28254439", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S984", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "O95714-1.995.995", "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": "O95714-1.1577.1577", "start_pos": 1577, "end_pos": 1577, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRVPKKPESTDDEEKIGNEE", "down_seq": "DLEEACILPHSPINVDKRPI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "site_lbl": "Ser1577" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "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": "O95714-1.1938.1938", "start_pos": 1938, "end_pos": 1938, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "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": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MGKEGKYDLKLAELPAAAQP", "down_seq": "AEDSDTEDDSEAEQTERNIH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser1938" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "O95714-1.1942.1942", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O95714-1.1944.1944", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O95714-1.1948.1948", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O95714-1.1951.1951", "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": "O95714-1.1944.1944", "start_pos": 1944, "end_pos": 1944, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "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": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YDLKLAELPAAAQPSAEDSD", "down_seq": "EDDSEAEQTERNIHPTAMMF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Thr1944" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O95714-1.1938.1938", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95714-1.1942.1942", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O95714-1.1948.1948", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O95714-1.1951.1951", "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": "O95714-1.1948.1948", "start_pos": 1948, "end_pos": 1948, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAELPAAAQPSAEDSDTEDD", "down_seq": "EAEQTERNIHPTAMMFTSTI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser1948" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O95714-1.1938.1938", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O95714-1.1942.1942", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O95714-1.1944.1944", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O95714-1.1951.1951", "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": "O95714-1.2454.2454", "start_pos": 2454, "end_pos": 2454, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ATTPVAVQHIRPARVKRRKQ", "down_seq": "PVPALPIVVQLMEMGFSRRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser2454" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "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": "O95714-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EVVERATRFLRSVVTGDVHG", "down_seq": "PATKGPGSIPLQDQHLALAI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "site_lbl": "Thr272" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O95714-1.274.274", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95714-1.2942.2942", "start_pos": 2942, "end_pos": 2942, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "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": "AVPFLASDNEEEEDEKGNSG", "down_seq": "LIRKKAAGLESAATIRTKVF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser2942" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O95714-1.2928.2928", "categories": [ "snv_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95714-1.4687.4687", "start_pos": 4687, "end_pos": 4687, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "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": "GYELETMVCGSPDIPLHLLK", "down_seq": "VATYKGIEPSASLIQWFWEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser4687" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O95714-1.4690.4690", "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": "O95714-1.4690.4690", "start_pos": 4690, "end_pos": 4690, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "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": "LETMVCGSPDIPLHLLKSVA", "down_seq": "YKGIEPSASLIQWFWEVMES", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr4690" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O95714-1.4687.4687", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O95714-1.4710.4710", "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": "O95714-1.4710.4710", "start_pos": 4710, "end_pos": 4710, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "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": "TYKGIEPSASLIQWFWEVME", "down_seq": "FSNTERSLFLRFVWGRTRLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser4710" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O95714-1.4690.4690", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O95714-1.4716.4716", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O95714-1.4726.4726", "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": "O95714-1.4810.4810", "start_pos": 4810, "end_pos": 4810, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SIDTDDYARIALTGEPAADD", "down_seq": "SDDSDNEDVDSFASDSTQDY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "site_lbl": "Ser4810" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O95714-1.4808.4808", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O95714-1.4809.4809", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O95714-1.4811.4811", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95714-1.4812.4812", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O95714-1.4814.4814", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O95714-1.4827.4827", "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": "O95714-1.4811.4811", "start_pos": 4811, "end_pos": 4811, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IDTDDYARIALTGEPAADDS", "down_seq": "DDSDNEDVDSFASDSTQDYL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "site_lbl": "Ser4811" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O95714-1.4808.4808", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95714-1.4809.4809", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O95714-1.4810.4810", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O95714-1.4812.4812", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O95714-1.4814.4814", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O95714-1.4827.4827", "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": "O95714-1.4814.4814", "start_pos": 4814, "end_pos": 4814, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DDYARIALTGEPAADDSSDD", "down_seq": "DNEDVDSFASDSTQDYLTGH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "site_lbl": "Ser4814" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O95714-1.4808.4808", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O95714-1.4809.4809", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O95714-1.4810.4810", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O95714-1.4811.4811", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95714-1.4812.4812", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O95714-1.4827.4827", "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": "O95714-1.647.647", "start_pos": 647, "end_pos": 647, "uniprot_canonical_ac": "O95714-1", "length": 4834, "uniprot_id": "HERC2_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HERC2", "refseq_ac": "NP_004658", "refseq_name": "E3 ubiquitin-protein ligase HERC2", "gene_name": "HERC2", "gene_names_uniprotkb": "HERC2", "gene_names_refseq": "D15F37S1; HERC2; MRT38; SHEP1; jdf2; p528", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" } ], "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": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] } ], "crossref": [ { "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "WSWGDGDYGKLGRGGSDGCK", "down_seq": "PKLIEKLQDLDVVKVRCGSQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O95714", "url": "https://www.uniprot.org/uniprotkb/O95714" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O95714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95714" } ], "site_lbl": "Thr647" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "2790", "end_pos": "2790" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "4022", "end_pos": "4022" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4182", "end_pos": "4182" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "2708", "end_pos": "2708" }, { "start_pos": "2711", "end_pos": "2711" }, { "start_pos": "4827", "end_pos": "4827" } ] }, { "type": "snv", "site_list": [ { "start_pos": "3487", "end_pos": "3487" }, { "start_pos": "3543", "end_pos": "3543" }, { "start_pos": "4628", "end_pos": "4628" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1056", "end_pos": "1056" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1386", "end_pos": "1386" }, { "start_pos": "1400", "end_pos": "1400" }, { "start_pos": "1428", "end_pos": "1428" }, { "start_pos": "1479", "end_pos": "1479" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1744", "end_pos": "1744" }, { "start_pos": "1771", "end_pos": "1771" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "1809", "end_pos": "1809" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2003", "end_pos": "2003" }, { "start_pos": "2031", "end_pos": "2031" }, { "start_pos": "2046", "end_pos": "2046" }, { "start_pos": "2085", "end_pos": "2085" }, { "start_pos": "2143", "end_pos": "2143" }, { "start_pos": "2151", "end_pos": "2151" }, { "start_pos": "2184", "end_pos": "2184" }, { "start_pos": "2185", "end_pos": "2185" }, { "start_pos": "2189", "end_pos": "2189" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2274", "end_pos": "2274" }, { "start_pos": "2290", "end_pos": "2290" }, { "start_pos": "2300", "end_pos": "2300" }, { "start_pos": "2333", "end_pos": "2333" }, { "start_pos": "2353", "end_pos": "2353" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "2504", "end_pos": "2504" }, { "start_pos": "2546", "end_pos": "2546" }, { "start_pos": "2630", "end_pos": "2630" }, { "start_pos": "2674", "end_pos": "2674" }, { "start_pos": "2707", "end_pos": "2707" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2757", "end_pos": "2757" }, { "start_pos": "2762", "end_pos": "2762" }, { "start_pos": "2768", "end_pos": "2768" }, { "start_pos": "2781", "end_pos": "2781" }, { "start_pos": "2792", "end_pos": "2792" }, { "start_pos": "2798", "end_pos": "2798" }, { "start_pos": "2841", "end_pos": "2841" }, { "start_pos": "2861", "end_pos": "2861" }, { "start_pos": "2870", "end_pos": "2870" }, { "start_pos": "2901", "end_pos": "2901" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "3030", "end_pos": "3030" }, { "start_pos": "3065", "end_pos": "3065" }, { "start_pos": "3136", "end_pos": "3136" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "3303", "end_pos": "3303" }, { "start_pos": "3310", "end_pos": "3310" }, { "start_pos": "3313", "end_pos": "3313" }, { "start_pos": "3331", "end_pos": "3331" }, { "start_pos": "3374", "end_pos": "3374" }, { "start_pos": "3438", "end_pos": "3438" }, { "start_pos": "3475", "end_pos": "3475" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "3485", "end_pos": "3485" }, { "start_pos": "3526", "end_pos": "3526" }, { "start_pos": "3544", "end_pos": "3544" }, { "start_pos": "3547", "end_pos": "3547" }, { "start_pos": "3554", "end_pos": "3554" }, { "start_pos": "3571", "end_pos": "3571" }, { "start_pos": "3575", "end_pos": "3575" }, { "start_pos": "3622", "end_pos": "3622" }, { "start_pos": "3623", "end_pos": "3623" }, { "start_pos": "3661", "end_pos": "3661" }, { "start_pos": "3665", "end_pos": "3665" }, { "start_pos": "3666", "end_pos": "3666" }, { "start_pos": "3675", "end_pos": "3675" }, { "start_pos": "3681", "end_pos": "3681" }, { "start_pos": "3700", "end_pos": "3700" }, { "start_pos": "3721", "end_pos": "3721" }, { "start_pos": "3744", "end_pos": "3744" }, { "start_pos": "3746", "end_pos": "3746" }, { "start_pos": "3748", "end_pos": "3748" }, { "start_pos": "3754", "end_pos": "3754" }, { "start_pos": "3793", "end_pos": "3793" }, { "start_pos": "3807", "end_pos": "3807" }, { "start_pos": "3906", "end_pos": "3906" }, { "start_pos": "3940", "end_pos": "3940" }, { "start_pos": "3945", "end_pos": "3945" }, { "start_pos": "4029", "end_pos": "4029" }, { "start_pos": "4075", "end_pos": "4075" }, { "start_pos": "4077", "end_pos": "4077" }, { "start_pos": "4183", "end_pos": "4183" }, { "start_pos": "4213", "end_pos": "4213" }, { "start_pos": "4238", "end_pos": "4238" }, { "start_pos": "4283", "end_pos": "4283" }, { "start_pos": "4355", "end_pos": "4355" }, { "start_pos": "4372", "end_pos": "4372" }, { "start_pos": "4374", "end_pos": "4374" }, { "start_pos": "4401", "end_pos": "4401" }, { "start_pos": "4410", "end_pos": "4410" }, { "start_pos": "4438", "end_pos": "4438" }, { "start_pos": "4476", "end_pos": "4476" }, { "start_pos": "4650", "end_pos": "4650" }, { "start_pos": "4716", "end_pos": "4716" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "4726", "end_pos": "4726" }, { "start_pos": "4769", "end_pos": "4769" }, { "start_pos": "4808", "end_pos": "4808" }, { "start_pos": "4809", "end_pos": "4809" }, { "start_pos": "4812", "end_pos": "4812" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "995", "end_pos": "995" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1938", "end_pos": "1938" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1944", "end_pos": "1944" }, { "start_pos": "1948", "end_pos": "1948" }, { "start_pos": "2454", "end_pos": "2454" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "2928", "end_pos": "2928" }, { "start_pos": "2942", "end_pos": "2942" }, { "start_pos": "4687", "end_pos": "4687" }, { "start_pos": "4690", "end_pos": "4690" }, { "start_pos": "4710", "end_pos": "4710" }, { "start_pos": "4810", "end_pos": "4810" }, { "start_pos": "4811", "end_pos": "4811" }, { "start_pos": "4814", "end_pos": "4814" }, { "start_pos": "4827", "end_pos": "4827" }, { "start_pos": "647", "end_pos": "647" } ] } ], "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": "Q9P2D6-1.1372.1372", "start_pos": 1372, "end_pos": 1372, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FLSLSGPHLGTLYNSSALVN", "down_seq": "GLWFMQKWKKSGSLLQLTCR", "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": "Thr1372", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q9P2D6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "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": "Q9P2D6-1.574.574", "start_pos": 574, "end_pos": 574, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1164127324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1164127324", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1164127324", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1164127324#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1164127324", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1164127324", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ICGYNFDPKTYMRQTSQKEA", "down_seq": "CLPTNTERTEQKSPDIENVQ", "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": "Ser574", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q9P2D6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "snv": [ { "evidence": [ { "id": "rs1164127324", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1164127324" }, { "id": "rs1164127324", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1164127324#frequency_tab" }, { "id": "rs1164127324", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1164127324" } ], "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": "6", "chr_pos": "70524805", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S574", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9P2D6-1.671.671", "start_pos": 671, "end_pos": 671, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "rs1362589251", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1362589251", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1362589251", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1362589251#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1362589251", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1362589251", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2128351911", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2128351911", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2128351911", "url": "https://www.ensembl.org/id/rs2128351911", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SLGVRTIEIKPSNKDPFSGE", "down_seq": "ITVKLGPWTELRQEEILVDN", "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": "DPFSGEnITVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn671", "evidence": [ { "id": "37074911", "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": "DPFSGEnITVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn671", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "snv": [ { "evidence": [ { "id": "rs1362589251", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1362589251" }, { "id": "rs1362589251", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1362589251#frequency_tab" }, { "id": "rs1362589251", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1362589251" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->DIT).", "chr_id": "6", "chr_pos": "70525095", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N671", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1362589251", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1362589251" }, { "id": "rs1362589251", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1362589251#frequency_tab" }, { "id": "rs1362589251", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1362589251" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->HIT).", "chr_id": "6", "chr_pos": "70525095", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N671", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2128351911", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2128351911" }, { "id": "rs2128351911", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2128351911" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->KIT).", "chr_id": "6", "chr_pos": "70525097", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N671", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "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": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9P2D6-1.744.744", "start_pos": 744, "end_pos": 744, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "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": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1794482103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1794482103", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1794482103", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1794482103", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SIGESLTKLRSNLPAPSTKE", "down_seq": "HVVVSGDTIKLPDISATYAS", "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": "Tyr744", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q9P2D6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ] } ], "snv": [ { "evidence": [ { "id": "rs1794482103", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1794482103" }, { "id": "rs1794482103", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1794482103" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (Y->*).", "chr_id": "6", "chr_pos": "70525316_70525317", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y744", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9P2D6-1.737.737", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9P2D6-1.749.749", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9P2D6-1.752.752", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9P2D6-1.759.759", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9P2D6-1.749.749", "start_pos": 749, "end_pos": 749, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] }, { "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": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LTKLRSNLPAPSTKEYHVVV", "down_seq": "GDTIKLPDISATYASSRFSD", "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": "Ser749", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q9P2D6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" }, { "id": "Q9P2D6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9P2D6-1.737.737", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9P2D6-1.744.744", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9P2D6-1.752.752", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9P2D6-1.759.759", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9P2D6-1.752.752", "start_pos": 752, "end_pos": 752, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "database": "O-GlcNAc Atlas", "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" } ], "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": "Q9P2D6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9P2D6", "url": "https://oglcnac.org/atlas/detail/Q9P2D6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1422725005", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1422725005", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1422725005", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1422725005", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LRSNLPAPSTKEYHVVVSGD", "down_seq": "IKLPDISATYASSRFSDSGV", "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": "Thr752", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q9P2D6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9P2D6" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q9P2D6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9P2D6" } ] } ], "snv": [ { "evidence": [ { "id": "rs1422725005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1422725005" }, { "id": "rs1422725005", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1422725005" } ], "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": "6", "chr_pos": "70525339", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T752", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9P2D6-1.737.737", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9P2D6-1.744.744", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9P2D6-1.749.749", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9P2D6-1.759.759", "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": "Q9P2D6-1.1017.1017", "start_pos": 1017, "end_pos": 1017, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765680467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765680467", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765680467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765680467", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765680467", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765680467#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765680467", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765680467", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKNSDVLNLTQMYSEIPTVE", "down_seq": "ETHLGTSDPFSASTDIVKQG", "snv": [ { "evidence": [ { "id": "rs765680467", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765680467" }, { "id": "rs765680467", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765680467" }, { "id": "rs765680467", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765680467#frequency_tab" }, { "id": "rs765680467", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765680467" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SET->NET).", "chr_id": "6", "chr_pos": "70526134", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1017", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.1045.1045", "start_pos": 1045, "end_pos": 1045, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs114229203", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114229203", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs114229203", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114229203", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs114229203", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114229203", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs114229203", "url": "https://www.ncbi.nlm.nih.gov/snp/rs114229203#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs114229203", "url": "http://gnomad.broadinstitute.org/awesome?query=rs114229203", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs114229203", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114229203", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DPFSASTDIVKQGLVENYFG", "down_seq": "QSSTDISDTCAVSYSNALSP", "snv": [ { "evidence": [ { "id": "rs114229203", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114229203" }, { "id": "rs114229203", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114229203" }, { "id": "rs114229203", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114229203" }, { "id": "rs114229203", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs114229203#frequency_tab" }, { "id": "rs114229203", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs114229203" }, { "id": "rs114229203", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114229203" } ], "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 (SQS->NQS).", "chr_id": "6", "chr_pos": "70559767", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1045", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.1099.1099", "start_pos": 1099, "end_pos": 1099, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1480150670", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1480150670", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1480150670", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1480150670", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QEQDKEDEEEEQDQQMVQNG", "down_seq": "YEETDYSALDGTINAHYTSR", "snv": [ { "evidence": [ { "id": "rs1480150670", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1480150670" }, { "id": "rs1480150670", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1480150670" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGY->NGC).", "chr_id": "6", "chr_pos": "70526380", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1099", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9P2D6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KMLLDERKIEETLEEMNFLL", "down_seq": "LDLHFTDGDYSADDLNALQL", "snv": [ { "evidence": [ { "id": "Q9P2D6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "70475700", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S112", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q9P2D6-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9P2D6-1.123.123", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.1182.1182", "start_pos": 1182, "end_pos": 1182, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764799595", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764799595", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764799595", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764799595", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764799595", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764799595#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764799595", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764799595", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPCNVKYSSKSKFDAITKQP", "down_seq": "STSYNFTSSISWYESSPKPQ", "snv": [ { "evidence": [ { "id": "rs764799595", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764799595" }, { "id": "rs764799595", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764799595" }, { "id": "rs764799595", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764799595#frequency_tab" }, { "id": "rs764799595", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764799595" } ], "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": "6", "chr_pos": "70526629", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1182", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9P2D6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MTEVQAMVEF", "down_seq": "VELNKFYNVDLFQRGFYQIR", "snv": [ { "evidence": [ { "id": "Q9P2D6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "6", "chr_pos": "70428373", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S11", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q9P2D6-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1247253047", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1247253047", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1247253047", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1247253047#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1247253047", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1247253047", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EETLEEMNFLLSLDLHFTDG", "down_seq": "YSADDLNALQLISSRTLKLH", "snv": [ { "evidence": [ { "id": "rs1247253047", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1247253047" }, { "id": "rs1247253047", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1247253047#frequency_tab" }, { "id": "rs1247253047", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1247253047" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DYS->NYS).", "chr_id": "6", "chr_pos": "70475726", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D121", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9P2D6-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9P2D6-1.123.123", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9P2D6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLEEMNFLLSLDLHFTDGDY", "down_seq": "ADDLNALQLISSRTLKLHFS", "snv": [ { "evidence": [ { "id": "Q9P2D6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "70475733", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S123", "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": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9P2D6-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9P2D6-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.1290.1290", "start_pos": 1290, "end_pos": 1290, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769511196", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769511196", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769511196", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769511196", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769511196", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769511196#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769511196", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769511196", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YIELGLPGGRIDFLMSERNQ", "down_seq": "DTFADFDSMTDRLLDEIIQY", "snv": [ { "evidence": [ { "id": "rs769511196", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769511196" }, { "id": "rs769511196", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769511196" }, { "id": "rs769511196", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769511196#frequency_tab" }, { "id": "rs769511196", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769511196" } ], "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 (NQN->NQS).", "chr_id": "6", "chr_pos": "70533758", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1290", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs769511196", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769511196" }, { "id": "rs769511196", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769511196" }, { "id": "rs769511196", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769511196#frequency_tab" }, { "id": "rs769511196", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769511196" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQN->NQT).", "chr_id": "6", "chr_pos": "70533758", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1290", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9P2D6-1.1327.1327", "start_pos": 1327, "end_pos": 1327, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9P2D6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IIQYIQIYSLTVSKISFIGH", "down_seq": "LGNLIIRSVLTRPRFKYYLN", "snv": [ { "evidence": [ { "id": "Q9P2D6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "6", "chr_pos": "70536274", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1327", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9P2D6-1.1332.1332", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.1332.1332", "start_pos": 1332, "end_pos": 1332, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1333420812", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1333420812", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1333420812", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1333420812#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1333420812", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1333420812", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "QIYSLTVSKISFIGHSLGNL", "down_seq": "IRSVLTRPRFKYYLNKLHTF", "snv": [ { "evidence": [ { "id": "rs1333420812", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1333420812" }, { "id": "rs1333420812", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1333420812#frequency_tab" }, { "id": "rs1333420812", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1333420812" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLI->NLT).", "chr_id": "6", "chr_pos": "70536289", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1332", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9P2D6-1.1327.1327", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.1409.1409", "start_pos": 1409, "end_pos": 1409, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755478533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755478533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755478533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755478533", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755478533", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755478533#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755478533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755478533", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LTCRDHSDPRQTFLYKLSNK", "down_seq": "GLHYFKNVVLVGSLQDRYVP", "snv": [ { "evidence": [ { "id": "rs755478533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755478533" }, { "id": "rs755478533", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755478533" }, { "id": "rs755478533", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755478533#frequency_tab" }, { "id": "rs755478533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755478533" } ], "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": "6", "chr_pos": "70538398", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1409", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.1498.1498", "start_pos": 1498, "end_pos": 1498, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9P2D6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALPNTADSLIGRAAHIAVLD", "down_seq": "EIFLEKFFLVAALKYFQ", "snv": [ { "evidence": [ { "id": "Q9P2D6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "70559866", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1498", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781729136", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781729136", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781729136", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781729136", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781729136", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781729136", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "SRTLKLHFSPHRGLHHHVNV", "down_seq": "FDYFHLSVVSVTVHASLVAL", "snv": [ { "evidence": [ { "id": "rs781729136", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781729136" }, { "id": "rs781729136", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781729136" }, { "id": "rs781729136", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781729136" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVM->NVT).", "chr_id": "6", "chr_pos": "70477254", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M155", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9P2D6-1.160.160", "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": "Q9P2D6-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1157950821", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1157950821", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1157950821", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1157950821", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LHFSPHRGLHHHVNVMFDYF", "down_seq": "LSVVSVTVHASLVALHQPLI", "snv": [ { "evidence": [ { "id": "rs1157950821", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1157950821" }, { "id": "rs1157950821", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1157950821" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HLS->NLS).", "chr_id": "6", "chr_pos": "70477268", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H160", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9P2D6-1.155.155", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs146974354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146974354", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs146974354", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146974354#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ALHQPLISFPRPVKTTWLNR", "down_seq": "APAQNKDSVIPTLESVVFGI", "snv": [ { "evidence": [ { "id": "rs146974354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146974354" }, { "id": "rs146974354", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146974354#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRN->NRS).", "chr_id": "6", "chr_pos": "70480939", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N194", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746917576", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746917576", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746917576", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746917576", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746917576", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746917576", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LCEEVKKIENPDELAELINM", "down_seq": "LAQLCSLLMALWGQFLEVIT", "snv": [ { "evidence": [ { "id": "rs746917576", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746917576" }, { "id": "rs746917576", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746917576" }, { "id": "rs746917576", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746917576" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NMN->NMS).", "chr_id": "6", "chr_pos": "70502679", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N306", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.542.542", "start_pos": 542, "end_pos": 542, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9P2D6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GYKCLKSTASNDLIKCFEGN", "down_seq": "SHSQKEGLDPTICGYNFDPK", "snv": [ { "evidence": [ { "id": "Q9P2D6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6" } ], "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": "6", "chr_pos": "70524708", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P542", "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": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.635.635", "start_pos": 635, "end_pos": 635, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750920559", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750920559", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750920559", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750920559", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750920559", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750920559", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9P2D6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SGKLDISQDDSEITQMEHNL", "down_seq": "SRRSSDDCHDHQTTPSLGVR", "snv": [ { "evidence": [ { "id": "rs750920559", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750920559" }, { "id": "rs750920559", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750920559" }, { "id": "rs750920559", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750920559" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLS).", "chr_id": "6", "chr_pos": "70524987", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A635", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9P2D6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9P2D6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLT).", "chr_id": "6", "chr_pos": "70524987", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A635", "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": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9P2D6-1.737.737", "start_pos": 737, "end_pos": 737, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs149282856", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149282856", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149282856", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149282856", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs149282856", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149282856", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149282856", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149282856#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149282856", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149282856", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LQEAKCLSIGESLTKLRSNL", "down_seq": "APSTKEYHVVVSGDTIKLPD", "snv": [ { "evidence": [ { "id": "rs149282856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149282856" }, { "id": "rs149282856", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149282856" }, { "id": "rs149282856", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149282856" }, { "id": "rs149282856", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149282856#frequency_tab" }, { "id": "rs149282856", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149282856" } ], "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": "6", "chr_pos": "70525293", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "P737", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs149282856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149282856" }, { "id": "rs149282856", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149282856" }, { "id": "rs149282856", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149282856" }, { "id": "rs149282856", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149282856#frequency_tab" }, { "id": "rs149282856", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149282856" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLP->NLT).", "chr_id": "6", "chr_pos": "70525293", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "P737", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q9P2D6-1.744.744", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9P2D6-1.749.749", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9P2D6-1.752.752", "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": "Q9P2D6-1.759.759", "start_pos": 759, "end_pos": 759, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1794489507", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1794489507", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1794489507", "url": "https://www.ensembl.org/id/rs1794489507", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSTKEYHVVVSGDTIKLPDI", "down_seq": "ATYASSRFSDSGVESEPSSF", "snv": [ { "evidence": [ { "id": "rs1794489507", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1794489507" }, { "id": "rs1794489507", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1794489507" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAT->NAT).", "chr_id": "6", "chr_pos": "70525360", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S759", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9P2D6-1.744.744", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9P2D6-1.749.749", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9P2D6-1.752.752", "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": "Q9P2D6-1.822.822", "start_pos": 822, "end_pos": 822, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1794524326", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1794524326", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1794524326", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1794524326#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "RLFPQLLMKPDYNVKFSLGN", "down_seq": "CTESTSAISEIQSSLTSINS", "snv": [ { "evidence": [ { "id": "rs1794524326", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1794524326" }, { "id": "rs1794524326", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1794524326#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HCT->NCT).", "chr_id": "6", "chr_pos": "70525548", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H822", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.889.889", "start_pos": 889, "end_pos": 889, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1273014470", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273014470", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1273014470", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1273014470#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1273014470", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1273014470", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KTVLNLGTTDLPKCDDTKKS", "down_seq": "ITLQQQSVVFSGNLDNETVA", "snv": [ { "evidence": [ { "id": "rs1273014470", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273014470" }, { "id": "rs1273014470", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1273014470#frequency_tab" }, { "id": "rs1273014470", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1273014470" } ], "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": "6", "chr_pos": "70525750", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S889", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9P2D6-1.986.986", "start_pos": 986, "end_pos": 986, "uniprot_canonical_ac": "Q9P2D6-1", "length": 1515, "uniprot_id": "F135A_HUMAN", "protein_name": "Protein FAM135A", "refseq_ac": "NP_001099001", "refseq_name": "protein FAM135A isoform a", "gene_name": "FAM135A", "gene_names_uniprotkb": "FAM135A; KIAA1411", "gene_names_refseq": "FAM135A; KIAA1411", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9P2D6", "url": "https://www.uniprot.org/uniprotkb/Q9P2D6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747394592", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747394592", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747394592", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747394592", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747394592", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747394592", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLNSKLICLGTPCVISGSIS", "down_seq": "NTDVSEDRTMKKNSDVLNLT", "snv": [ { "evidence": [ { "id": "rs747394592", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747394592" }, { "id": "rs747394592", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747394592" }, { "id": "rs747394592", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747394592" } ], "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": "6", "chr_pos": "70538390", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S986", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1372", "end_pos": "1372" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "752", "end_pos": "752" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1017", "end_pos": "1017" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1099", "end_pos": "1099" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1182", "end_pos": "1182" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1327", "end_pos": "1327" }, { "start_pos": "1332", "end_pos": "1332" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "737", "end_pos": "737" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" }, { "database": "O-GlcNAc Atlas", "id": "Q8WU58", "url": "https://oglcnac.org/atlas/detail/Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "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": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2034904932", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034904932", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2034904932", "url": "https://www.ensembl.org/id/rs2034904932", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2034904932", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2034904932", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDLSSIVHQINQFCQTRAGI", "down_seq": "TTSVCEGQIANPSPISRSLL", "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": "Ser283", "evidence": [ { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q8WU58", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" } ] } ], "snv": [ { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" }, { "id": "rs2034904932", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034904932" }, { "id": "rs2034904932", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2034904932" }, { "id": "rs2034904932", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2034904932" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->G).", "chr_id": "17", "chr_pos": "28759112", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S283", "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": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q8WU58-1.299.299", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WU58-1.299.299", "start_pos": 299, "end_pos": 299, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" }, { "database": "O-GlcNAc Atlas", "id": "Q8WU58", "url": "https://oglcnac.org/atlas/detail/Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "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": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WU58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "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": "Q8WU58", "url": "https://oglcnac.org/atlas/detail/Q8WU58", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2034899947", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034899947", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2034899947", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034899947#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RAGISTTSVCEGQIANPSPI", "down_seq": "RSLLINASTRVSTHSVPTPM", "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": "Ser299", "evidence": [ { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q8WU58", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WU58" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "Q8WU58", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8WU58" } ] } ], "snv": [ { "evidence": [ { "id": "rs2034899947", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034899947" }, { "id": "rs2034899947", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034899947#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (SRS->NRS); o-glyco-site-loss (S->N).", "chr_id": "17", "chr_pos": "28759063", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S299", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->G).", "chr_id": "17", "chr_pos": "28759064", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S299", "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": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8WU58-1.283.283", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WU58-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "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": "rs1439680557", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439680557", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1439680557", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1439680557", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1597836782", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1597836782", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1597836782", "url": "https://www.ensembl.org/id/rs1597836782", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MNTGLQKWDTTQKMRTAHYP", "down_seq": "PAELDAYAKKVANNPLTIKI", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr41", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1439680557", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439680557" }, { "id": "rs1439680557", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1439680557" } ], "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": "28759837", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T41", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1597836782", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1597836782" }, { "id": "rs1597836782", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1597836782" } ], "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": "28759838", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T41", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "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": "Q8WU58-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "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": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1206624801", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1206624801", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1206624801", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1206624801", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1597829701", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1597829701", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1597829701", "url": "https://www.ensembl.org/id/rs1597829701", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YPQELCLAQSFHLKPPLEKP", "down_seq": "PSPPVNGMAAPLAYPNGHYF", "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": "Thr430", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" } ], "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": "17", "chr_pos": "28758671", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T430", "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": "rs1206624801", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1206624801" }, { "id": "rs1206624801", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1206624801" } ], "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": "28758670", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T430", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1597829701", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1597829701" }, { "id": "rs1597829701", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1597829701" } ], "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": "28758671", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T430", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "Q8WU58-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "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": "rs1170062728", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170062728", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1170062728", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170062728", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HVRRTVNGLDTSAQRYSPYP", "down_seq": "QAATKAGLLAIVKVPAKSIL", "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": "Thr93", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1170062728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170062728" }, { "id": "rs1170062728", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170062728" } ], "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": "28759682", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T93", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8WU58-1.82.82", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1309532690", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309532690", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309532690", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309532690#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1309532690", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309532690", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1309532690", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1309532690", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TKAGLLAIVKVPAKSILKDF", "down_seq": "GTRARLLPEAIMNPPVAPYA", "snv": [ { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" }, { "id": "rs1309532690", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309532690" }, { "id": "rs1309532690", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309532690#frequency_tab" }, { "id": "rs1309532690", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309532690" }, { "id": "rs1309532690", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1309532690" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DGT->NGT).", "chr_id": "17", "chr_pos": "28759610", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D117", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PQALAHQGLQHPHNPLLHGG", "down_seq": "KMPDSDAPPNVTVSTSTIPL", "snv": [ { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" } ], "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": "17", "chr_pos": "28759268", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R231", "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": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.346.346", "start_pos": 346, "end_pos": 346, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PMEHTHAATAALPAAGPVNL", "down_seq": "TGISRVPTGYPSDLKPVTWN", "snv": [ { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" } ], "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 (NLP->NLS).", "chr_id": "17", "chr_pos": "28758923", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P346", "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": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2034871941", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034871941", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2034871941", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034871941#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPVTWNQHQLAHLQQMCSEA", "down_seq": "GTPAPGLTGKHAAGRELAGP", "snv": [ { "evidence": [ { "id": "rs2034871941", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034871941" }, { "id": "rs2034871941", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034871941#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 (SGT->NGT).", "chr_id": "17", "chr_pos": "28758817", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S381", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2034847317", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034847317", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2034847317", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034847317#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "GMAAPLAYPNGHYFQPLWNN", "down_seq": "LPTPNSDSSGSQDLAMPFHG", "snv": [ { "evidence": [ { "id": "rs2034847317", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034847317" }, { "id": "rs2034847317", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034847317#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNI->NNT).", "chr_id": "17", "chr_pos": "28758589", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I457", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q8WU58-1.464.464", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1269817968", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269817968", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1269817968", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1269817968#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1269817968", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269817968", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YPNGHYFQPLWNNILPTPNS", "down_seq": "SSGSQDLAMPFHGGQPTGAP", "snv": [ { "evidence": [ { "id": "rs1269817968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269817968" }, { "id": "rs1269817968", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1269817968#frequency_tab" }, { "id": "rs1269817968", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269817968" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "17", "chr_pos": "28758569", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D464", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8WU58-1.457.457", "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": "Q8WU58-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAPGAHYRAGTGGGPVASQN", "down_seq": "LMQTVDYLSGDFQQACFREQ", "snv": [ { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" } ], "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": "17", "chr_pos": "28758432", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S509", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q8WU58-1.551.551", "start_pos": 551, "end_pos": 551, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WU58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAMLSKAHRAPGNRAPDPTE", "down_seq": "RSLHIQHPGYR", "snv": [ { "evidence": [ { "id": "Q8WU58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WU58" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SRS->NRS).", "chr_id": "17", "chr_pos": "28758307", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S551", "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": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WU58-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "Q8WU58-1", "length": 562, "uniprot_id": "F222B_HUMAN", "protein_name": "Protein FAM222B", "refseq_ac": "NP_001070966", "refseq_name": "protein FAM222B isoform 2", "gene_name": "FAM222B", "gene_names_uniprotkb": "FAM222B; C17orf63", "gene_names_refseq": "C17orf63; FAM222B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WU58", "url": "https://www.uniprot.org/uniprotkb/Q8WU58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1241486054", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241486054", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1241486054", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1241486054", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FPNSVKVPQRKHVRRTVNGL", "down_seq": "TSAQRYSPYPTQAATKAGLL", "snv": [ { "evidence": [ { "id": "rs1241486054", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241486054" }, { "id": "rs1241486054", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1241486054" } ], "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": "17", "chr_pos": "28759715", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D82", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "283", "end_pos": "283" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "snv", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q8WU58-1.93.93", "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": "Q86XA9-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "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": "Q86XA9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86XA9" } ], "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": "Q86XA9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86XA9", "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": "Q86XA9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86XA9" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "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": "Q86XA9-1.1257.1257", "start_pos": 1257, "end_pos": 1257, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ANSAHFDIALAQEMKKRDSR", "down_seq": "DFLVLHLADLIRMAFMAATD", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "14", "chr_pos": "31321680", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N1257", "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:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q86XA9-1.1269.1269", "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": "Q86XA9-1.1269.1269", "start_pos": 1269, "end_pos": 1269, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EMKKRDSRNDFLVLHLADLI", "down_seq": "MAFMAATDHSDQLRLSGLEM", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "14", "chr_pos": "31321645", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1269", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q86XA9-1.1257.1257", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86XA9-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SKLLGIILAKAVISKHPGTA", "down_seq": "SRQSIRRVSLEEVLELLGTG", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "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 (3).", "chr_id": "14", "chr_pos": "31389003", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A253", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID: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": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86XA9-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KATQTQIDAVCCRRCVSFIL", "down_seq": "TTIGGLLGEKAQLAAVKDIC", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "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 (4).", "chr_id": "14", "chr_pos": "31387212", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R360", "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: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": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86XA9-1.393.393", "start_pos": 393, "end_pos": 393, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LAAVKDICQAIWKLKKVMDA", "down_seq": "MSDGNLETRLGSTDVAASQH", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "14", "chr_pos": "31386570", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V393", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID: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": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86XA9-1.484.484", "start_pos": 484, "end_pos": 484, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AWCLHCIAVALPSYLTPLLD", "down_seq": "CLERLTGHKSSPEAVTGFSF", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "14", "chr_pos": "31383649", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R484", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86XA9-1.757.757", "start_pos": 757, "end_pos": 757, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEQLLLGNGVACGSLEYDPY", "down_seq": "IYEKDVEGDSVPKPLPPALS", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "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": "14", "chr_pos": "31358760", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S757", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID: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": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86XA9-1.932.932", "start_pos": 932, "end_pos": 932, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86XA9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LALGSLHRYLGGISSSQHLN", "down_seq": "CIGILYTLAQDSTSPDVQTW", "snv": [ { "evidence": [ { "id": "Q86XA9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86XA9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "5", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "14", "chr_pos": "31347821", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S932", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86XA9-1.1110.1110", "start_pos": 1110, "end_pos": 1110, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "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": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" }, { "database": "iPTMnet", "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLVQREAAEVSEHAVMLAKD", "down_seq": "REELTPDANIREVGLEGALL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9" } ], "site_lbl": "Ser1110" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q86XA9-1.1115.1115", "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": "Q86XA9-1.1115.1115", "start_pos": 1115, "end_pos": 1115, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "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": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" }, { "database": "iPTMnet", "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EAAEVSEHAVMLAKDSREEL", "down_seq": "PDANIREVGLEGALLILLDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9" } ], "site_lbl": "Thr1115" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q86XA9-1.1110.1110", "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": "Q86XA9-1.1647.1647", "start_pos": 1647, "end_pos": 1647, "uniprot_canonical_ac": "Q86XA9-1", "length": 2040, "uniprot_id": "HTR5A_HUMAN", "protein_name": "HEAT repeat-containing protein 5A", "refseq_ac": "NP_056288", "refseq_name": "HEAT repeat-containing protein 5A", "gene_name": "HEATR5A", "gene_names_uniprotkb": "HEATR5A; C14orf125; KIAA1316", "gene_names_refseq": "C14orf125; HEATR5A; p200b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" } ], "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": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" }, { "database": "iPTMnet", "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LEVVRQIICAAQEHVKEKRR", "down_seq": "AEVDDGAAEKETLPEFGEGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q86XA9", "url": "https://www.uniprot.org/uniprotkb/Q86XA9" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q86XA9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86XA9" } ], "site_lbl": "Ser1647" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1257", "end_pos": "1257" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "932", "end_pos": "932" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1647", "end_pos": "1647" } ] } ], "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": "Q9ULQ1-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "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": "VVQFVEAIVVLVRQMSHVRV", "down_seq": "RALRCIFLVDCRYCGGVRRN", "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": "Thr201", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q9ULQ1-1.219.223", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9ULQ1-1.599.599", "start_pos": 599, "end_pos": 599, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YSFAIVGMEFFCGIVFPNCC", "down_seq": "TSTVADAYRWRNHTVGNRTV", "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": "Asn599", "evidence": [ { "id": "Q9ULQ1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9ULQ1-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9ULQ1-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9ULQ1-1.612.612", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9ULQ1-1.616.616", "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": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9ULQ1-1.611.611", "start_pos": 611, "end_pos": 611, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "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": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1", "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": "rs993929421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs993929421", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs993929421", "url": "https://www.ncbi.nlm.nih.gov/snp/rs993929421#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GIVFPNCCNTSTVADAYRWR", "down_seq": "HTVGNRTVVEEGYYYLNNFD", "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": "Asn611", "evidence": [ { "id": "Q9ULQ1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1#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": "rs993929421", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs993929421" }, { "id": "rs993929421", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs993929421#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHT->SHT).", "chr_id": "12", "chr_pos": "113290163", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N611", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9ULQ1-1.599.599", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9ULQ1-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9ULQ1-1.612.612", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9ULQ1-1.616.616", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9ULQ1-1.630.630", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9ULQ1-1.616.616", "start_pos": 616, "end_pos": 616, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "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": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1", "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": "rs773363205", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773363205", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773363205", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773363205", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773363205", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773363205", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NCCNTSTVADAYRWRNHTVG", "down_seq": "RTVVEEGYYYLNNFDNILNS", "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": "Asn616", "evidence": [ { "id": "Q9ULQ1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1#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": "rs773363205", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773363205" }, { "id": "rs773363205", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773363205" }, { "id": "rs773363205", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773363205" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->SRT).", "chr_id": "12", "chr_pos": "113290178", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N616", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9ULQ1-1.599.599", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9ULQ1-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9ULQ1-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9ULQ1-1.612.612", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9ULQ1-1.630.630", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9ULQ1-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "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": "Q9ULQ1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9ULQ1" } ], "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": "Q9ULQ1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9ULQ1", "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": "Q9ULQ1", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9ULQ1" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "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": "Q9ULQ1-1.219.223", "start_pos": 219, "end_pos": 223, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The voltage-gated sodium channel TPC1 confers endolysosomal excitability.", "journal": "Nature chemical biology", "date": "2014", "authors": "Cang C, Bekele B, Ren D", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "reference": [ { "type": "PubMed", "id": "24776928", "url": "https://glygen.org/publication/PubMed/24776928" } ] } ], "crossref": [ { "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24776928", "url": "https://glygen.org/publication/PubMed/24776928", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "RRNLR", "start_aa": "R", "up_seq": "RVTRALRCIFLVDCRYCGGV", "down_seq": "QIFQSLPPFMDILLLLLFFM", "mutagenesis": [ { "sequence_org": "RRNLR", "sequence_mut": "QQNLQ", "comment": "Loss of voltage sensitivity.", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" }, { "database": "PubMed", "id": "24776928", "url": "https://glygen.org/publication/PubMed/24776928" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9ULQ1-1.201.201", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9ULQ1-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Essential requirement for two-pore channel 1 in NAADP-mediated calcium signaling.", "journal": "The Journal of cell biology", "date": "2009", "authors": "Brailoiu E, Churamani D, Cai X, Schrlau MG, Brailoiu GC, Gao X, Hooper R, Boulware MJ, Dun NJ, Marchant JS, Patel S", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" }, { "database": "Reactome", "id": "R-HSA-2672351", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2672351" }, { "database": "RefSeq", "id": "NP_001137291", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001137291" } ], "reference": [ { "type": "PubMed", "id": "19620632", "url": "https://glygen.org/publication/PubMed/19620632" } ] } ], "crossref": [ { "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19620632", "url": "https://glygen.org/publication/PubMed/19620632", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LFSPNPSDPYFSTLENSIVS", "down_seq": "FVLLTTANFPDVMMPSYSRN", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "P", "comment": "Loss of NAADP-mediated cytoplasmic calcium release.", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" }, { "database": "PubMed", "id": "19620632", "url": "https://glygen.org/publication/PubMed/19620632" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9ULQ1-1.258.258", "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": "Q9ULQ1-1.539.539", "start_pos": 539, "end_pos": 539, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The voltage-gated sodium channel TPC1 confers endolysosomal excitability.", "journal": "Nature chemical biology", "date": "2014", "authors": "Cang C, Bekele B, Ren D", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "reference": [ { "type": "PubMed", "id": "24776928", "url": "https://glygen.org/publication/PubMed/24776928" } ] } ], "crossref": [ { "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24776928", "url": "https://glygen.org/publication/PubMed/24776928", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FLGLLALALNMEPFYFIVVL", "down_seq": "PLQLLRLFKLKERYRNVLDT", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "I", "comment": "Loss of voltage sensitivity.", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" }, { "database": "PubMed", "id": "24776928", "url": "https://glygen.org/publication/PubMed/24776928" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q9ULQ1-1.536.536", "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": "Q9ULQ1-1.740.741", "start_pos": 740, "end_pos": 741, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An NAADP-gated two-pore channel targeted to the plasma membrane uncouples triggering from amplifying Ca2+ signals.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Brailoiu E, Rahman T, Churamani D, Prole DL, Brailoiu GC, Hooper R, Taylor CW, Patel S", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "reference": [ { "type": "PubMed", "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839" } ] } ], "crossref": [ { "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "LL", "start_aa": "L", "up_seq": "LVAVLELYREARGASSDVTR", "down_seq": "ETLSQMERYQQHSMVFLGRR", "mutagenesis": [ { "sequence_org": "LL", "sequence_mut": "AA", "comment": "No effect on subcellular location.", "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" }, { "database": "PubMed", "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9ULQ1-1.743.743", "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": "Q9ULQ1-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1265127963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265127963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1265127963", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1265127963#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LLLFFMIIFAILGFYLFSPN", "down_seq": "SDPYFSTLENSIVSLFVLLT", "snv": [ { "evidence": [ { "id": "rs1265127963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265127963" }, { "id": "rs1265127963", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1265127963#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NSS).", "chr_id": "12", "chr_pos": "113272681", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P258", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q9ULQ1-1.273.273", "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": "Q9ULQ1-1.392.392", "start_pos": 392, "end_pos": 392, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770258651", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770258651", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770258651", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770258651", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770258651", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770258651#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770258651", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770258651", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PRMSARERYLTFKALNQNNT", "down_seq": "LLSLKDFYDIYEVAALKWKA", "snv": [ { "evidence": [ { "id": "rs770258651", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770258651" }, { "id": "rs770258651", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770258651" }, { "id": "rs770258651", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770258651#frequency_tab" }, { "id": "rs770258651", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770258651" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTP->NTS).", "chr_id": "12", "chr_pos": "113277354", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P392", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9ULQ1-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9ULQ1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9ULQ1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs138959802", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138959802", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138959802", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138959802", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs138959802", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138959802", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs138959802", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138959802#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs138959802", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138959802", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SAPLAPSNGLGQEELPSKNG", "down_seq": "SYAIHDSQAPSLSSGGESSP", "snv": [ { "evidence": [ { "id": "Q9ULQ1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9ULQ1" }, { "id": "rs138959802", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138959802" }, { "id": "rs138959802", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138959802" }, { "id": "rs138959802", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138959802" }, { "id": "rs138959802", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138959802#frequency_tab" }, { "id": "rs138959802", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138959802" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGG->NGS).", "chr_id": "12", "chr_pos": "113260373", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G40", "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": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9ULQ1-1.51.51", "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": "Q9ULQ1-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1250081983", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250081983", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1250081983", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1250081983#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1250081983", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250081983", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1250081983", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1250081983", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QEELPSKNGGSYAIHDSQAP", "down_seq": "LSSGGESSPSSPAHNWEMNY", "snv": [ { "evidence": [ { "id": "rs1250081983", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250081983" }, { "id": "rs1250081983", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1250081983#frequency_tab" }, { "id": "rs1250081983", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250081983" }, { "id": "rs1250081983", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1250081983" } ], "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 (SLS->NLS).", "chr_id": "12", "chr_pos": "113260407", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S51", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9ULQ1-1.40.40", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9ULQ1-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9ULQ1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9ULQ1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VFAFLGLLALALNMEPFYFI", "down_seq": "VLRPLQLLRLFKLKERYRNV", "snv": [ { "evidence": [ { "id": "Q9ULQ1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9ULQ1" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "113287066", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V536", "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: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": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q9ULQ1-1.539.539", "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": "Q9ULQ1-1.601.601", "start_pos": 601, "end_pos": 601, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1249630298", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249630298", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1249630298", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249630298", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs748983271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748983271", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748983271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748983271", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748983271", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748983271#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748983271", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748983271", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FAIVGMEFFCGIVFPNCCNT", "down_seq": "TVADAYRWRNHTVGNRTVVE", "snv": [ { "evidence": [ { "id": "rs1249630298", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249630298" }, { "id": "rs1249630298", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249630298" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->NTG).", "chr_id": "12", "chr_pos": "113290132", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S601", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748983271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748983271" }, { "id": "rs748983271", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748983271" }, { "id": "rs748983271", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748983271#frequency_tab" }, { "id": "rs748983271", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748983271" } ], "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 (NTS->NTN).", "chr_id": "12", "chr_pos": "113290133", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S601", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9ULQ1-1.599.599", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9ULQ1-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9ULQ1-1.612.612", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9ULQ1-1.616.616", "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": "Q9ULQ1-1.612.612", "start_pos": 612, "end_pos": 612, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777347185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777347185", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777347185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777347185", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777347185", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777347185", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IVFPNCCNTSTVADAYRWRN", "down_seq": "TVGNRTVVEEGYYYLNNFDN", "snv": [ { "evidence": [ { "id": "rs777347185", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777347185" }, { "id": "rs777347185", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777347185" }, { "id": "rs777347185", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777347185" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHT->NPT).", "chr_id": "12", "chr_pos": "113290166", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H612", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9ULQ1-1.599.599", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9ULQ1-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9ULQ1-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9ULQ1-1.616.616", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9ULQ1-1.630.630", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9ULQ1-1.630.630", "start_pos": 630, "end_pos": 630, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1170924264", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170924264", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1170924264", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1170924264#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1170924264", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170924264", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "RNHTVGNRTVVEEGYYYLNN", "down_seq": "DNILNSFVTLFELTVVNNWY", "snv": [ { "evidence": [ { "id": "rs1170924264", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170924264" }, { "id": "rs1170924264", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1170924264#frequency_tab" }, { "id": "rs1170924264", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170924264" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNF->NNS).", "chr_id": "12", "chr_pos": "113290220", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F630", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9ULQ1-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9ULQ1-1.612.612", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9ULQ1-1.616.616", "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": "Q9ULQ1-1.743.743", "start_pos": 743, "end_pos": 743, "uniprot_canonical_ac": "Q9ULQ1-1", "length": 816, "uniprot_id": "TPC1_HUMAN", "protein_name": "Two pore channel protein 1", "refseq_ac": "NP_001137291", "refseq_name": "two pore channel protein 1 isoform 1", "gene_name": "TPCN1", "gene_names_uniprotkb": "TPCN1; KIAA1169; TPC1", "gene_names_refseq": "TPC1; TPCN1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9ULQ1", "url": "https://www.uniprot.org/uniprotkb/Q9ULQ1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1456024715", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456024715", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1456024715", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456024715#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1456024715", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456024715", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VLELYREARGASSDVTRLLE", "down_seq": "LSQMERYQQHSMVFLGRRSR", "snv": [ { "evidence": [ { "id": "rs1456024715", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456024715" }, { "id": "rs1456024715", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456024715#frequency_tab" }, { "id": "rs1456024715", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456024715" } ], "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": "113293048", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T743", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "201", "end_pos": "201" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "616", "end_pos": "616" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "219", "end_pos": "223" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "740", "end_pos": "741" } ] }, { "type": "snv", "site_list": [ { "start_pos": "258", "end_pos": "258" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "743", "end_pos": "743" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9ULQ1-1.740.741", "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": "Q9GZU8-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "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": "Q9GZU8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9GZU8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9GZU8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9GZU8", "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": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q9GZU8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9GZU8" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q9GZU8-1.17.17", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9GZU8-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28gamma.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Jonik-Nowak B, Menneteau T, Fesquet D, Baldin V, Bonne-Andrea C, Mechali F, Fabre B, Boisguerin P, de Rossi S, Henriquet C, Pugniere M, Ducoux-Petit M, Burlet-Schiltz O, Lamond AI, Fort P, Boulon S, Bousquet MP, Coux O", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "RefSeq", "id": "NP_079222", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_079222" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "crossref": [ { "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CPSAAVCIGILPGLGAYSGS", "down_seq": "DSESSSDSEGTINATGKIVS", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Reduces phosphorylation by CK2 and interaction with PSME3; when associated with A-228.", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CK2", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" }, { "database": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ], "site_lbl": "Ser222" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9GZU8-1.223.225", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9GZU8-1.228.228", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9GZU8-1.229.231", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9GZU8-1.242.242", "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": "Q9GZU8-1.223.225", "start_pos": 223, "end_pos": 225, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28gamma.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Jonik-Nowak B, Menneteau T, Fesquet D, Baldin V, Bonne-Andrea C, Mechali F, Fabre B, Boisguerin P, de Rossi S, Henriquet C, Pugniere M, Ducoux-Petit M, Burlet-Schiltz O, Lamond AI, Fort P, Boulon S, Bousquet MP, Coux O", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "RefSeq", "id": "NP_079222", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_079222" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "crossref": [ { "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DSE", "start_aa": "D", "up_seq": "PSAAVCIGILPGLGAYSGSS", "down_seq": "SSSDSEGTINATGKIVSSIF", "mutagenesis": [ { "sequence_org": "DSE", "sequence_mut": "KSK", "comment": "Abolishes phosphorylation by CK2, strongly reduces interaction with PSME3 and abolishes effect on proteasome activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9GZU8-1.222.222", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9GZU8-1.228.228", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9GZU8-1.229.231", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9GZU8-1.242.242", "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": "Q9GZU8-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28gamma.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Jonik-Nowak B, Menneteau T, Fesquet D, Baldin V, Bonne-Andrea C, Mechali F, Fabre B, Boisguerin P, de Rossi S, Henriquet C, Pugniere M, Ducoux-Petit M, Burlet-Schiltz O, Lamond AI, Fort P, Boulon S, Bousquet MP, Coux O", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "RefSeq", "id": "NP_079222", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_079222" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "crossref": [ { "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CIGILPGLGAYSGSSDSESS", "down_seq": "DSEGTINATGKIVSSIFRTN", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Reduces phosphorylation by CK2 and interaction with PSME3; when associated with A-222.", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CK2", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" }, { "database": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ], "site_lbl": "Ser228" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9GZU8-1.222.222", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9GZU8-1.223.225", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9GZU8-1.229.231", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9GZU8-1.242.242", "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": "Q9GZU8-1.229.231", "start_pos": 229, "end_pos": 231, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28gamma.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Jonik-Nowak B, Menneteau T, Fesquet D, Baldin V, Bonne-Andrea C, Mechali F, Fabre B, Boisguerin P, de Rossi S, Henriquet C, Pugniere M, Ducoux-Petit M, Burlet-Schiltz O, Lamond AI, Fort P, Boulon S, Bousquet MP, Coux O", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "RefSeq", "id": "NP_079222", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_079222" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "crossref": [ { "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DSE", "start_aa": "D", "up_seq": "IGILPGLGAYSGSSDSESSS", "down_seq": "GTINATGKIVSSIFRTNTFL", "mutagenesis": [ { "sequence_org": "DSE", "sequence_mut": "KSK", "comment": "Strongly reduces phosphorylation by CK2 and interaction with PSME3.", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "PubMed", "id": "29934401", "url": "https://glygen.org/publication/PubMed/29934401" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9GZU8-1.222.222", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9GZU8-1.223.225", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9GZU8-1.228.228", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9GZU8-1.242.242", "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": "Q9GZU8-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9GZU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9GZU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VSEAELDERRKRRQEEWEKV", "down_seq": "KPEDPEECPEEVYDPRSLYE", "snv": [ { "evidence": [ { "id": "Q9GZU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9GZU8" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "57173749", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R36", "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": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9GZU8-1.17.17", "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": "Q9GZU8-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "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": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MDGGDDGNLIIKKRFV", "down_seq": "EAELDERRKRRQEEWEKVRK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" } ], "site_lbl": "Ser17" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9GZU8-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9GZU8-1.36.36", "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": "Q9GZU8-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "Q9GZU8-1", "length": 254, "uniprot_id": "PIP30_HUMAN", "protein_name": "PSME3-interacting protein", "refseq_ac": "NP_079222", "refseq_name": "PSME3-interacting protein isoform a", "gene_name": "PSME3IP1", "gene_names_uniprotkb": "PSME3IP1; C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30", "gene_names_refseq": "C16orf94; CDA018; CDA10; FAM192A; NIP30; PIP30; PSME3IP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9GZU8", "url": "https://www.uniprot.org/uniprotkb/Q9GZU8" } ], "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": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8", "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": "SDSESSSDSEGTINATGKIV", "down_seq": "SIFRTNTFLEAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9GZU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9GZU8" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser242" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "225" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "231" } ] }, { "type": "snv", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "242", "end_pos": "242" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9GZU8-1.222.222", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9GZU8-1.223.225", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9GZU8-1.228.228", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9GZU8-1.229.231", "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": "P50213-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "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": "rs2074723691", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074723691", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2074723691", "url": "https://www.ensembl.org/id/rs2074723691", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NLYGDILSDLCAGLIGGLGV", "down_seq": "PSGNIGANGVAIFESVHGTA", "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": "Thr273", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs2074723691", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074723691" }, { "id": "rs2074723691", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2074723691" } ], "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": "15", "chr_pos": "78165030", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T273", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50213-1.255.255", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50213-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P50213", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P50213" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "P50213", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P50213" }, { "database": "O-GlcNAc Atlas", "id": "P50213", "url": "https://oglcnac.org/atlas/detail/P50213" } ], "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": "P50213", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P50213" } ], "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": "P50213", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P50213" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P50213", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P50213" } ], "reference": [ { "type": "PubMed", "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054" } ] } ], "crossref": [ { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P50213", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P50213", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "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": "34229054", "url": "https://glygen.org/publication/PubMed/34229054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P50213", "url": "https://oglcnac.org/atlas/detail/P50213", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AVMKIFDAAKAPIQWEERNV", "down_seq": "AIQGPGGKWMIPSEAKESMD", "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": "Thr69", "evidence": [ { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "P50213", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P50213" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "34229054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34229054" }, { "id": "P50213", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P50213" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P50213-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.", "journal": "Scientific reports", "date": "2017", "authors": "Ma T, Peng Y, Huang W, Ding J", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "reference": [ { "type": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GYKTPYTDVNIVTIRENTEG", "down_seq": "YSGIEHVIVDGVVQSIKLIT", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "No significant effect on the activation of the heterodimer composed of IDH3A and IDH3G subunits by citrate and ADP.", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P50213-1.153.153", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50213-1.169.169", "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": "P50213-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The beta and gamma subunits play distinct functional roles in the alpha2betagamma heterotetramer of human NAD-dependent isocitrate dehydrogenase.", "journal": "Scientific reports", "date": "2017", "authors": "Ma T, Peng Y, Huang W, Liu Y, Ding J", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "reference": [ { "type": "PubMed", "id": "28139779", "url": "https://glygen.org/publication/PubMed/28139779" } ] } ], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28139779", "url": "https://glygen.org/publication/PubMed/28139779", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YKTPYTDVNIVTIRENTEGE", "down_seq": "SGIEHVIVDGVVQSIKLITE", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Complete loss of activity of the heterotetramer, heterodimer composed of IDH3A and IDH3B subunits and the heterodimer composed of IDH3A and IDH3G subunits with no effect on their oligomeric states.", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "PubMed", "id": "28139779", "url": "https://glygen.org/publication/PubMed/28139779" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P50213-1.152.152", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50213-1.169.169", "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": "P50213-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.", "journal": "Scientific reports", "date": "2017", "authors": "Ma T, Peng Y, Huang W, Ding J", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "reference": [ { "type": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TEGEYSGIEHVIVDGVVQSI", "down_seq": "LITEGASKRIAEFAFEYARN", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Significantly impairs the activation of the heterodimer composed of IDH3A and IDH3G subunits by citrate and ADP.", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P50213-1.152.152", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50213-1.153.153", "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": "P50213-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.", "journal": "Scientific reports", "date": "2017", "authors": "Ma T, Peng Y, Huang W, Ding J", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "reference": [ { "type": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AEFAFEYARNNHRSNVTAVH", "down_seq": "ANIMRMSDGLFLQKCREVAE", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Significantly impairs the activation of the heterodimer composed of IDH3A and IDH3G subunits by citrate.", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P50213-1.202.202", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50213-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50213-1.208.208", "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": "P50213-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.", "journal": "Scientific reports", "date": "2017", "authors": "Ma T, Peng Y, Huang W, Ding J", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "reference": [ { "type": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FAFEYARNNHRSNVTAVHKA", "down_seq": "IMRMSDGLFLQKCREVAESC", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Significantly impairs the activation of the heterodimer composed of IDH3A and IDH3G subunits by citrate.", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P50213-1.200.200", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50213-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50213-1.208.208", "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": "P50213-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.", "journal": "Scientific reports", "date": "2017", "authors": "Ma T, Peng Y, Huang W, Ding J", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "reference": [ { "type": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RNNHRSNVTAVHKANIMRMS", "down_seq": "GLFLQKCREVAESCKDIKFN", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Complete loss of the activation of the heterodimer composed of IDH3A and IDH3G subunits by citrate and ADP.", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P50213-1.200.200", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50213-1.202.202", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50213-1.204.204", "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": "P50213-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.", "journal": "Scientific reports", "date": "2017", "authors": "Ma T, Peng Y, Huang W, Ding J", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "reference": [ { "type": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VCLNMVQDPSQFDVLVMPNL", "down_seq": "GDILSDLCAGLIGGLGVTPS", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Significantly impairs the activation of the heterodimer composed of IDH3A and IDH3G subunits by citrate and ADP.", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "PubMed", "id": "28098230", "url": "https://glygen.org/publication/PubMed/28098230" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P50213-1.273.273", "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": "P50213-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2074690463", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074690463", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2074690463", "url": "https://www.ensembl.org/id/rs2074690463", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "FEYARNNHRSNVTAVHKANI", "down_seq": "RMSDGLFLQKCREVAESCKD", "snv": [ { "evidence": [ { "id": "rs2074690463", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074690463" }, { "id": "rs2074690463", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2074690463" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIM->NIT).", "chr_id": "15", "chr_pos": "78162367", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M204", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P50213-1.200.200", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50213-1.202.202", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50213-1.208.208", "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": "P50213-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Homozygous mutation, p.Pro304His, in IDH3A, encoding isocitrate dehydrogenase subunit is associated with severe encephalopathy in infancy.", "journal": "Neurogenetics", "date": "2017", "authors": "Fattal-Valevski A, Eliyahu H, Fraenkel ND, Elmaliach G, Hausman-Kedem M, Shaag A, Mandel D, Pines O, Elpeleg O", "evidence": [ { "database": "dbSNP", "id": "rs756712426", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756712426" } ], "reference": [ { "type": "PubMed", "id": "28058510", "url": "https://glygen.org/publication/PubMed/28058510" } ] }, { "title": "Whole-Exome Sequencing Identifies Biallelic IDH3A Variants as a Cause of Retinitis Pigmentosa Accompanied by Pseudocoloboma.", "journal": "Ophthalmology", "date": "2017", "authors": "Pierrache LHM, Kimchi A, Ratnapriya R, Roberts L, Astuti GDN, Obolensky A, Beryozkin A, Tjon-Fo-Sang MJH, Schuil J, Klaver CCW, Bongers EMHF, Haer-Wigman L, Schalij N, Breuning MH, Fischer GM, Banin E, Ramesar RS, Swaroop A, van den Born LI, Sharon D, Cremers FPM", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" }, { "database": "dbSNP", "id": "rs756712426", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756712426" } ], "reference": [ { "type": "PubMed", "id": "28412069", "url": "https://glygen.org/publication/PubMed/28412069" } ] } ], "crossref": [ { "id": "rs756712426", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756712426", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756712426", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756712426", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756712426", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756712426", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "28058510", "url": "https://glygen.org/publication/PubMed/28058510", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28412069", "url": "https://glygen.org/publication/PubMed/28412069", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs2074740525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074740525", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2074740525", "url": "https://www.ensembl.org/id/rs2074740525", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2074740525", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2074740525", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "P50213", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50213", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AIFESVHGTAPDIAGKDMAN", "down_seq": "TALLLSAVMMLRHMGLFDHA", "snv": [ { "evidence": [ { "id": "rs756712426", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756712426" }, { "id": "rs756712426", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756712426" }, { "id": "rs756712426", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756712426" }, { "id": "28058510", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28058510" }, { "id": "28412069", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28412069" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NHT).", "chr_id": "15", "chr_pos": "78166196", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P304", "disease": [ { "disease_id": "DOID:10584", "recommended_name": { "id": "DOID:10584", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10584", "name": "retinitis pigmentosa", "description": "A retinal degeneration characterized by the gradual deterioration of the photoreceptors or the retinal pigment epithelium of the retina leading to progressive sight loss." }, "synonyms": [ { "id": "DOID:10584", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10584", "name": "pericentral pigmentary retinopathy", "description": "" }, { "id": "MONDO:0019200", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019200", "name": "retinitis pigmentosa", "description": "Retinitis pigmentosa (RP) is an inherited retinal dystrophy leading to progressive loss of the photoreceptors and retinal pigment epithelium and resulting in blindness usually after several decades." }, { "id": "MONDO:0019200", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019200", "name": "retinitis pigmentosa", "description": "" }, { "id": "MONDO:0019200", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019200", "name": "pericentral pigmentary retinopathy", "description": "" }, { "id": "MONDO:0019200", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019200", "name": "Rod-cone dystrophy", "description": "" }, { "id": "MIM:268000", "resource": "MIM", "url": "https://www.omim.org/entry/268000", "name": "Retinitis pigmentosa", "description": "Retinitis pigmentosa" } ], "unlinked_id_list": [], "evidence": [ { "id": "10584", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10584" } ] }, { "disease_id": "DOID:0112147", "recommended_name": { "id": "DOID:0112147", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0112147", "name": "retinitis pigmentosa 90", "description": "A retinitis pigmentosa characterized by onset in the first decade of life of night blindness that has_material_basis_in homozygous or compound heterozygous mutation in the IDH3A gene on chromosome 15q25.1." }, "synonyms": [ { "id": "DOID:0112147", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0112147", "name": "RP90", "description": "" }, { "id": "MONDO:0033563", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0033563", "name": "retinitis pigmentosa 90", "description": "" }, { "id": "MONDO:0033563", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0033563", "name": "RP90", "description": "" }, { "id": "MIM:619007", "resource": "MIM", "url": "https://www.omim.org/entry/619007", "name": "Retinitis pigmentosa 90", "description": "Retinitis pigmentosa 90" } ], "unlinked_id_list": [], "evidence": [ { "id": "619007", "database": "MIM", "url": "https://www.omim.org/entry/619007" }, { "id": "0112147", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0112147" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2074740525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074740525" }, { "id": "rs2074740525", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2074740525" }, { "id": "rs2074740525", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2074740525" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPT->NST).", "chr_id": "15", "chr_pos": "78166195", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P304", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "P50213", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50213" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPT->NTT).", "chr_id": "15", "chr_pos": "78166195", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P304", "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": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P50213-1.364.364", "start_pos": 364, "end_pos": 364, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50213", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50213", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DLGGNAKCSDFTEEICRRVK", "down_seq": "LD", "snv": [ { "evidence": [ { "id": "P50213", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50213" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "78168994", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D364", "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": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50213-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSEAKESMDKNKMGLKGPLK", "down_seq": "PIAAGHPSMNLLLRKTFDLY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "site_lbl": "Thr101" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P50213-1.117.117", "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": "P50213-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P50213-1", "length": 366, "uniprot_id": "IDH3A_HUMAN", "protein_name": "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial", "refseq_ac": "NP_005521", "refseq_name": "isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor", "gene_name": "IDH3A", "gene_names_uniprotkb": "IDH3A", "gene_names_refseq": "IDH3A; RP90", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50213", "url": "https://www.uniprot.org/uniprotkb/P50213" } ], "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": "P50213-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P50213-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P50213", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P50213", "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": "GPLKTPIAAGHPSMNLLLRK", "down_seq": "FDLYANVRPCVSIEGYKTPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P50213", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P50213" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr117" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "273", "end_pos": "273" }, { "start_pos": "69", "end_pos": "69" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "255", "end_pos": "255" } ] }, { "type": "snv", "site_list": [ { "start_pos": "204", "end_pos": "204" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "364", "end_pos": "364" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "117", "end_pos": "117" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P50213-1.101.101", "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": "Q5W0V3-1.553.553", "start_pos": 553, "end_pos": 553, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "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": "DISPENTLPNQEWLSSSPPA", "down_seq": "PDHPKNDGKTEVHKIVNSFL", "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": "Thr553", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q5W0V3-1.540.540", "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": "Q5W0V3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "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": "Q5W0V3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5W0V3" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q5W0V3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5W0V3" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5W0V3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5W0V3", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q5W0V3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5W0V3" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "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": "Q5W0V3-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs938838410", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs938838410", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs938838410", "url": "https://www.ensembl.org/id/rs938838410", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "IQFLCIVCAKLKQDPYLVNF", "down_seq": "LENKMKSLASKGVPNVISED", "snv": [ { "evidence": [ { "id": "rs938838410", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs938838410" }, { "id": "rs938838410", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs938838410" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFF->NFC).", "chr_id": "10", "chr_pos": "114836239", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q5W0V3-1.177.177", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1450849658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450849658", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1450849658", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1450849658", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "IVCAKLKQDPYLVNFFLENK", "down_seq": "KSLASKGVPNVISEDTLKGQ", "snv": [ { "evidence": [ { "id": "rs1450849658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450849658" }, { "id": "rs1450849658", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1450849658" } ], "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": "10", "chr_pos": "114842940", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M177", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q5W0V3-1.172.172", "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": "Q5W0V3-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KSLASKGVPNVISEDTLKGQ", "down_seq": "SLSTDTGQSRQPEELSGATG", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "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": "10", "chr_pos": "114843002", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D198", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELEDEPPHQMDHLSTSLDNL", "down_seq": "VTSLPEASVVCPNQDYNLVN", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SVT->NVT).", "chr_id": "10", "chr_pos": "114843138", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S243", "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": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GRIAVKACEGLMLLVSLPEP", "down_seq": "AAKCLTQSTCLCELLTDRLA", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "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": "10", "chr_pos": "114843804", "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: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": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q5W0V3-1.302.302", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756315959", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756315959", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756315959", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756315959", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756315959", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756315959", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGLMLLVSLPEPAAAKCLTQ", "down_seq": "TCLCELLTDRLASLYKALPQ", "snv": [ { "evidence": [ { "id": "rs756315959", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756315959" }, { "id": "rs756315959", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756315959" }, { "id": "rs756315959", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756315959" } ], "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 (STC->NTC).", "chr_id": "10", "chr_pos": "114843829", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S302", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q5W0V3-1.294.294", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CELLTDRLASLYKALPQSVD", "down_seq": "LDIETVEAINWGLDSYSHKE", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "10", "chr_pos": "114843901", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P326", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.347.347", "start_pos": 347, "end_pos": 347, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs926511216", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs926511216", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs926511216", "url": "https://www.ncbi.nlm.nih.gov/snp/rs926511216#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs926511216", "url": "http://gnomad.broadinstitute.org/awesome?query=rs926511216", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LDIETVEAINWGLDSYSHKE", "down_seq": "ASAFPGKRALISFLSWFDYC", "snv": [ { "evidence": [ { "id": "rs926511216", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs926511216" }, { "id": "rs926511216", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs926511216#frequency_tab" }, { "id": "rs926511216", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs926511216" } ], "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": "10", "chr_pos": "114845392", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D347", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q5W0V3-1.365.365", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.365.365", "start_pos": 365, "end_pos": 365, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2083695348", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2083695348", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2083695348", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2083695348#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KEDASAFPGKRALISFLSWF", "down_seq": "YCDQLIKEAQKTAAVALAKA", "snv": [ { "evidence": [ { "id": "rs2083695348", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2083695348" }, { "id": "rs2083695348", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2083695348#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DYC->NYC).", "chr_id": "10", "chr_pos": "114845446", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D365", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q5W0V3-1.347.347", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.540.540", "start_pos": 540, "end_pos": 540, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2083706294", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2083706294", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2083706294", "url": "https://www.ensembl.org/id/rs2083706294", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AGAVDLEEDPLFTDISPENT", "down_seq": "PNQEWLSSSPPATPDHPKND", "snv": [ { "evidence": [ { "id": "rs2083706294", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2083706294" }, { "id": "rs2083706294", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2083706294" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTL->NTS).", "chr_id": "10", "chr_pos": "114847140", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L540", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q5W0V3-1.553.553", "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": "Q5W0V3-1.579.579", "start_pos": 579, "end_pos": 579, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NDGKTEVHKIVNSFLCLVPD", "down_seq": "AKSSYHVEGTGYDTYLRDAH", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "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 (3).", "chr_id": "10", "chr_pos": "114848670", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D579", "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:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "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": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q5W0V3-1.580.580", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.580.580", "start_pos": 580, "end_pos": 580, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DGKTEVHKIVNSFLCLVPDD", "down_seq": "KSSYHVEGTGYDTYLRDAHR", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "114848672", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A580", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q5W0V3-1.579.579", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.603.603", "start_pos": 603, "end_pos": 603, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SYHVEGTGYDTYLRDAHRQF", "down_seq": "DYCAICLRWEWPGSPKALEK", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "114855200", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R603", "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: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": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5W0V3-1.684.684", "start_pos": 684, "end_pos": 684, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs146879041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146879041", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs146879041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146879041", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs146879041", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146879041#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs146879041", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146879041", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs146879041", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146879041", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LSLFPHPHIHEYLLDPYVNL", "down_seq": "PGCRSLFSVIVRVVGDLMLR", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLS).", "chr_id": "10", "chr_pos": "114860851", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A684", "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": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" }, { "id": "rs146879041", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146879041" }, { "id": "rs146879041", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146879041" }, { "id": "rs146879041", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146879041#frequency_tab" }, { "id": "rs146879041", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146879041" }, { "id": "rs146879041", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146879041" } ], "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 (NLA->NLT).", "chr_id": "10", "chr_pos": "114860851", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A684", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q5W0V3-1.755.755", "start_pos": 755, "end_pos": 755, "uniprot_canonical_ac": "Q5W0V3-1", "length": 765, "uniprot_id": "FHI2A_HUMAN", "protein_name": "FHF complex subunit HOOK interacting protein 2A", "refseq_ac": "NP_001128523", "refseq_name": "FHF complex subunit HOOK interacting protein 2A isoform b", "gene_name": "FHIP2A", "gene_names_uniprotkb": "FHIP2A; FAM160B1; KIAA1600", "gene_names_refseq": "FAM160B1; FHIP2A; KIAA1600; bA106M7.3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5W0V3", "url": "https://www.uniprot.org/uniprotkb/Q5W0V3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5W0V3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ITLLEGVIVLEEFCKELAAI", "down_seq": "FVKYHASSTP", "snv": [ { "evidence": [ { "id": "Q5W0V3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5W0V3" } ], "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 (6).", "chr_id": "10", "chr_pos": "114861505", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A755", "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: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:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "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": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "172", "end_pos": "172" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "755", "end_pos": "755" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15034-1.1013.1013", "start_pos": 1013, "end_pos": 1013, "uniprot_canonical_ac": "Q15034-1", "length": 1050, "uniprot_id": "HERC3_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase HERC3", "refseq_ac": "NP_001258531", "refseq_name": "probable E3 ubiquitin-protein ligase HERC3 isoform 2", "gene_name": "HERC3", "gene_names_uniprotkb": "HERC3; KIAA0032", "gene_names_refseq": "HERC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15034", "url": "https://www.uniprot.org/uniprotkb/Q15034" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15034", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YGMASLQIVIQSTASGEEYL", "down_seq": "VAHTCYNLLDLPKYSSKEIL", "snv": [ { "evidence": [ { "id": "Q15034", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034" } ], "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": "4", "chr_pos": "88706845", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1013", "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: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": "1013", "end_pos": "1013" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "846", "end_pos": "846" }, { "start_pos": "851", "end_pos": "851" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15034-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "Q15034-1", "length": 1050, "uniprot_id": "HERC3_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase HERC3", "refseq_ac": "NP_001258531", "refseq_name": "probable E3 ubiquitin-protein ligase HERC3 isoform 2", "gene_name": "HERC3", "gene_names_uniprotkb": "HERC3; KIAA0032", "gene_names_refseq": "HERC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15034", "url": "https://www.uniprot.org/uniprotkb/Q15034" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15034", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AHSFALSLSGAVFGWGMNNA", "down_seq": "QLGLSDEKDRESPCHVKLLR", "snv": [ { "evidence": [ { "id": "Q15034", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "88653063", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G220", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1013", "end_pos": "1013" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "846", "end_pos": "846" }, { "start_pos": "851", "end_pos": "851" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15034-1.358.358", "start_pos": 358, "end_pos": 358, "uniprot_canonical_ac": "Q15034-1", "length": 1050, "uniprot_id": "HERC3_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase HERC3", "refseq_ac": "NP_001258531", "refseq_name": "probable E3 ubiquitin-protein ligase HERC3 isoform 2", "gene_name": "HERC3", "gene_names_uniprotkb": "HERC3; KIAA0032", "gene_names_refseq": "HERC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15034", "url": "https://www.uniprot.org/uniprotkb/Q15034" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15034", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PSPVKGYWAAHSGQLSARAD", "down_seq": "FKYHIVKQIFSGGDQTFVLC", "snv": [ { "evidence": [ { "id": "Q15034", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034" } ], "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": "4", "chr_pos": "88658417", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R358", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "1013", "end_pos": "1013" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "846", "end_pos": "846" }, { "start_pos": "851", "end_pos": "851" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15034-1.539.539", "start_pos": 539, "end_pos": 539, "uniprot_canonical_ac": "Q15034-1", "length": 1050, "uniprot_id": "HERC3_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase HERC3", "refseq_ac": "NP_001258531", "refseq_name": "probable E3 ubiquitin-protein ligase HERC3 isoform 2", "gene_name": "HERC3", "gene_names_uniprotkb": "HERC3; KIAA0032", "gene_names_refseq": "HERC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15034", "url": "https://www.uniprot.org/uniprotkb/Q15034" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15034", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SKYYITLTIPLAMAILRLDT", "down_seq": "PSKVLDNWWSQVCPKYFMKL", "snv": [ { "evidence": [ { "id": "Q15034", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "N", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "88668063", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N539", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1013", "end_pos": "1013" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "846", "end_pos": "846" }, { "start_pos": "851", "end_pos": "851" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q15034-1.748.748", "start_pos": 748, "end_pos": 748, "uniprot_canonical_ac": "Q15034-1", "length": 1050, "uniprot_id": "HERC3_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase HERC3", "refseq_ac": "NP_001258531", "refseq_name": "probable E3 ubiquitin-protein ligase HERC3 isoform 2", "gene_name": "HERC3", "gene_names_uniprotkb": "HERC3; KIAA0032", "gene_names_refseq": "HERC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15034", "url": "https://www.uniprot.org/uniprotkb/Q15034" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15034", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KKPLKVIFDGEEAVDAGGVT", "down_seq": "EFFLLLLKELLNPIYGMFTY", "snv": [ { "evidence": [ { "id": "Q15034", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "88680140", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K748", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1013", "end_pos": "1013" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "846", "end_pos": "846" }, { "start_pos": "851", "end_pos": "851" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15034-1.846.846", "start_pos": 846, "end_pos": 846, "uniprot_canonical_ac": "Q15034-1", "length": 1050, "uniprot_id": "HERC3_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase HERC3", "refseq_ac": "NP_001258531", "refseq_name": "probable E3 ubiquitin-protein ligase HERC3 isoform 2", "gene_name": "HERC3", "gene_names_uniprotkb": "HERC3; KIAA0032", "gene_names_refseq": "HERC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15034", "url": "https://www.uniprot.org/uniprotkb/Q15034" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15034", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DLKELSPTEGRSLQELLDYP", "down_seq": "EDVEETFCLNFTICRESYGV", "snv": [ { "evidence": [ { "id": "Q15034", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "88686764", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G846", "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: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": "1013", "end_pos": "1013" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "846", "end_pos": "846" }, { "start_pos": "851", "end_pos": "851" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q15034-1.851.851", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15034-1.851.851", "start_pos": 851, "end_pos": 851, "uniprot_canonical_ac": "Q15034-1", "length": 1050, "uniprot_id": "HERC3_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase HERC3", "refseq_ac": "NP_001258531", "refseq_name": "probable E3 ubiquitin-protein ligase HERC3 isoform 2", "gene_name": "HERC3", "gene_names_uniprotkb": "HERC3; KIAA0032", "gene_names_refseq": "HERC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15034", "url": "https://www.uniprot.org/uniprotkb/Q15034" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15034", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SPTEGRSLQELLDYPGEDVE", "down_seq": "TFCLNFTICRESYGVIEQKK", "snv": [ { "evidence": [ { "id": "Q15034", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15034" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "88686780", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E851", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1013", "end_pos": "1013" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "846", "end_pos": "846" }, { "start_pos": "851", "end_pos": "851" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q15034-1.846.846", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q9BZF9-1.706.706", "start_pos": 706, "end_pos": 706, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "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": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification.", "journal": "Talanta", "date": "2017", "authors": "Shen B, Zhang W, Shi Z, Tian F, Deng Y, Sun C, Wang G, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" } ], "reference": [ { "type": "PubMed", "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811" } ] }, { "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": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" } ], "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": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" } ], "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": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" } ], "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": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" }, { "database": "O-GlcNAc Atlas", "id": "Q9BZF9", "url": "https://oglcnac.org/atlas/detail/Q9BZF9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BZF9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BZF9", "url": "https://oglcnac.org/atlas/detail/Q9BZF9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EHEQVKSRLEQKSGELGKKI", "down_seq": "ELTLKNQTLQKEIEKVYLDN", "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": "Thr706", "evidence": [ { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q9BZF9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BZF9" }, { "id": "28411811", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28411811" }, { "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": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q9BZF9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9BZF9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9BZF9-1.712.712", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BZF9-1.714.714", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BZF9-1.723.723", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BZF9-1.712.712", "start_pos": 712, "end_pos": 712, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "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": "SRLEQKSGELGKKITELTLK", "down_seq": "QTLQKEIEKVYLDNKLLKEQ", "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": "NQTLQKEIEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn712", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9BZF9-1.706.706", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BZF9-1.714.714", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BZF9-1.723.723", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BZF9-1.1015.1015", "start_pos": 1015, "end_pos": 1015, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201129903", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201129903", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201129903", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201129903", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201129903", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201129903", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201129903", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201129903#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201129903", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201129903", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201129903", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201129903", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ERKFKATEKELKDQLSEQTQ", "down_seq": "YSVSEEEVKKNKQENDKLKK", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" }, { "id": "rs201129903", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201129903" }, { "id": "rs201129903", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201129903" }, { "id": "rs201129903", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201129903" }, { "id": "rs201129903", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201129903#frequency_tab" }, { "id": "rs201129903", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201129903" }, { "id": "rs201129903", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201129903" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KYS->NYS).", "chr_id": "15", "chr_pos": "70667639", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1015", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1074.1074", "start_pos": 1074, "end_pos": 1074, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs61729919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61729919", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61729919", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61729919", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61729919", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61729919#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61729919", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61729919", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SHEMERALSRKTDELNKQLK", "down_seq": "LSQKYTEVKNVKEKLVEENA", "snv": [ { "evidence": [ { "id": "rs61729919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61729919" }, { "id": "rs61729919", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61729919" }, { "id": "rs61729919", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61729919#frequency_tab" }, { "id": "rs61729919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61729919" } ], "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": "15", "chr_pos": "70667464", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00981162", "site_lbl": "D1074", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9BZF9-1.1065.1065", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BZF9-1.1077.1077", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1077.1077", "start_pos": 1077, "end_pos": 1077, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MERALSRKTDELNKQLKDLS", "down_seq": "KYTEVKNVKEKLVEENAKQT", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "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": "15", "chr_pos": "70667453", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q1077", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9BZF9-1.1065.1065", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BZF9-1.1074.1074", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1160.1160", "start_pos": 1160, "end_pos": 1160, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RCYEKEQQTVTKLHQLLENQ", "down_seq": "NSSVPLAEHLQIKEAFEKEV", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "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 (KNS->NNS).", "chr_id": "15", "chr_pos": "70667204", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K1160", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1198.1198", "start_pos": 1198, "end_pos": 1198, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1159174060", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159174060", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1159174060", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1159174060", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KEVGIIKASLREKEEESQNK", "down_seq": "EEVSKLQSEVQNTKQALKKL", "snv": [ { "evidence": [ { "id": "rs1159174060", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159174060" }, { "id": "rs1159174060", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1159174060" } ], "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": "15", "chr_pos": "70667091", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1198", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q9BZF9-1.1212.1212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1212.1212", "start_pos": 1212, "end_pos": 1212, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EESQNKMEEVSKLQSEVQNT", "down_seq": "QALKKLETREVVDLSKYKAT", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTK->NTT).", "chr_id": "15", "chr_pos": "70667049", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K1212", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9BZF9-1.1198.1198", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BZF9-1.1225.1225", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1225.1225", "start_pos": 1225, "end_pos": 1225, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1373580260", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373580260", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1373580260", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1373580260", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QSEVQNTKQALKKLETREVV", "down_seq": "LSKYKATKSDLETQISSLNE", "snv": [ { "evidence": [ { "id": "rs1373580260", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373580260" }, { "id": "rs1373580260", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1373580260" } ], "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": "15", "chr_pos": "70667011", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1225", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9BZF9-1.1212.1212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1251.1251", "start_pos": 1251, "end_pos": 1251, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1294587299", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294587299", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1294587299", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294587299", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ATKSDLETQISSLNEKLANL", "down_seq": "RKYEEVCEEVLHAKKKEISA", "snv": [ { "evidence": [ { "id": "rs1294587299", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294587299" }, { "id": "rs1294587299", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294587299" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLN->NLS).", "chr_id": "15", "chr_pos": "70666932", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1251", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLN->NLT).", "chr_id": "15", "chr_pos": "70666932", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N1251", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BZF9-1.1253.1253", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9BZF9-1.1253.1253", "start_pos": 1253, "end_pos": 1253, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201992560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201992560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201992560", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201992560", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201992560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201992560", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201992560", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201992560#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201992560", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201992560", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KSDLETQISSLNEKLANLNR", "down_seq": "YEEVCEEVLHAKKKEISAKD", "snv": [ { "evidence": [ { "id": "rs201992560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201992560" }, { "id": "rs201992560", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201992560" }, { "id": "rs201992560", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201992560" }, { "id": "rs201992560", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201992560#frequency_tab" }, { "id": "rs201992560", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201992560" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRK->NRT).", "chr_id": "15", "chr_pos": "70666926", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "K1253", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BZF9-1.1251.1251", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1897895469", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1897895469", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1897895469", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1897895469#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "HLAAKYGHALCLQKLLQYNC", "down_seq": "TEHADLQGRTALHDAAMADC", "snv": [ { "evidence": [ { "id": "rs1897895469", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1897895469" }, { "id": "rs1897895469", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1897895469#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCP->NCS).", "chr_id": "15", "chr_pos": "70690502", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P126", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NCP->NCT).", "chr_id": "15", "chr_pos": "70690502", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P126", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9BZF9-1.224.224", "start_pos": 224, "end_pos": 224, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs536787451", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536787451", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs536787451", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536787451", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs536787451", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536787451", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs536787451", "url": "http://gnomad.broadinstitute.org/awesome?query=rs536787451", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LMLGCEYGCRDAVEVLIKNG", "down_seq": "DISLLDALGHDSSYYARIGD", "snv": [ { "evidence": [ { "id": "rs536787451", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536787451" }, { "id": "rs536787451", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536787451" }, { "id": "rs536787451", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536787451" }, { "id": "rs536787451", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs536787451" } ], "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": "15", "chr_pos": "70684379", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "A224", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9BZF9-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BZF9-1.241.241", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1384841660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1384841660", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1384841660", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1384841660#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AVEVLIKNGADISLLDALGH", "down_seq": "SSYYARIGDNLDILTLLKTA", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" }, { "id": "rs1384841660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1384841660" }, { "id": "rs1384841660", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1384841660#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "15", "chr_pos": "70684346", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D235", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9BZF9-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BZF9-1.241.241", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KNGADISLLDALGHDSSYYA", "down_seq": "IGDNLDILTLLKTASENTNK", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "70684327", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R241", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BZF9-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BZF9-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BZF9-1.260.260", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.260.260", "start_pos": 260, "end_pos": 260, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs975711700", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs975711700", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs975711700", "url": "https://www.ncbi.nlm.nih.gov/snp/rs975711700#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs975711700", "url": "http://gnomad.broadinstitute.org/awesome?query=rs975711700", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ARIGDNLDILTLLKTASENT", "down_seq": "KGRELWKKGPSLQQRNLTHM", "snv": [ { "evidence": [ { "id": "rs975711700", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs975711700" }, { "id": "rs975711700", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs975711700#frequency_tab" }, { "id": "rs975711700", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs975711700" } ], "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": "15", "chr_pos": "70684270", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N260", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9BZF9-1.241.241", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "AAKEKQHEESLRTIEALKNR", "down_seq": "KYFESDHLGSGSHFSNRKED", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRF->NRC).", "chr_id": "15", "chr_pos": "70676506", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F373", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q9BZF9-1.386.386", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IEALKNRFKYFESDHLGSGS", "down_seq": "FSNRKEDMLLKQGQMYMADS", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HFS->NFS).", "chr_id": "15", "chr_pos": "70671977", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H386", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9BZF9-1.373.373", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200591121", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200591121", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200591121", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200591121", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200591121", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200591121#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200591121", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200591121", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GIPAHMQSRSMLRPLELSLP", "down_seq": "QTSYSENEILKKELEAMRTF", "snv": [ { "evidence": [ { "id": "rs200591121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200591121" }, { "id": "rs200591121", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200591121" }, { "id": "rs200591121", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200591121#frequency_tab" }, { "id": "rs200591121", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200591121" } ], "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": "15", "chr_pos": "70669389", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S432", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BZF9-1.434.434", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BZF9-1.435.435", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BZF9-1.450.450", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.450.450", "start_pos": 450, "end_pos": 450, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LPSQTSYSENEILKKELEAM", "down_seq": "TFCESAKQDRLKLQNELAHK", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "15", "chr_pos": "70669335", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R450", "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: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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BZF9-1.432.432", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9BZF9-1.434.434", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9BZF9-1.435.435", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BZF9-1.460.460", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EILKKELEAMRTFCESAKQD", "down_seq": "LKLQNELAHKVAECKALALE", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "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": "15", "chr_pos": "70669306", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R460", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BZF9-1.450.450", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.537.537", "start_pos": 537, "end_pos": 537, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769084461", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769084461", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769084461", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769084461", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QTHFLALKEHLTSEAASGNH", "down_seq": "LTEELKDQLKDLKVKYEGAS", "snv": [ { "evidence": [ { "id": "rs769084461", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769084461" }, { "id": "rs769084461", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769084461" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHR->NHT).", "chr_id": "15", "chr_pos": "70669074", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R537", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.567.567", "start_pos": 567, "end_pos": 567, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1897039950", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1897039950", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1897039950", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1897039950", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KDLKVKYEGASAEVGKLRNQ", "down_seq": "KQNEMIVEEFKRDEGKLIEE", "snv": [ { "evidence": [ { "id": "rs1897039950", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1897039950" }, { "id": "rs1897039950", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1897039950" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQI->NQT).", "chr_id": "15", "chr_pos": "70668984", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I567", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.714.714", "start_pos": 714, "end_pos": 714, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1897018644", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1897018644", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1897018644", "url": "https://www.ensembl.org/id/rs1897018644", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LEQKSGELGKKITELTLKNQ", "down_seq": "LQKEIEKVYLDNKLLKEQAH", "snv": [ { "evidence": [ { "id": "rs1897018644", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1897018644" }, { "id": "rs1897018644", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1897018644" } ], "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 (NQT->NQA).", "chr_id": "15", "chr_pos": "70668544", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T714", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BZF9-1.706.706", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BZF9-1.712.712", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BZF9-1.723.723", "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": "Q9BZF9-1.744.744", "start_pos": 744, "end_pos": 744, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774430262", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774430262", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774430262", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774430262", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774430262", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774430262#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774430262", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774430262", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LDNKLLKEQAHNLTIEMKNH", "down_seq": "VPLKVSEDMKKSHDAIIDDL", "snv": [ { "evidence": [ { "id": "rs774430262", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774430262" }, { "id": "rs774430262", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774430262" }, { "id": "rs774430262", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774430262#frequency_tab" }, { "id": "rs774430262", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774430262" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHY->NHC).", "chr_id": "15", "chr_pos": "70668453", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y744", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774430262", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774430262" }, { "id": "rs774430262", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774430262" }, { "id": "rs774430262", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774430262#frequency_tab" }, { "id": "rs774430262", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774430262" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHY->NHS).", "chr_id": "15", "chr_pos": "70668453", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y744", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9BZF9-1.795.795", "start_pos": 795, "end_pos": 795, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1322815679", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1322815679", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1322815679", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1322815679#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1322815679", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1322815679", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YTEKKLEMEKLLLENDSLSK", "down_seq": "VSRLETVFVPPEKHEKEIIA", "snv": [ { "evidence": [ { "id": "rs1322815679", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1322815679" }, { "id": "rs1322815679", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1322815679#frequency_tab" }, { "id": "rs1322815679", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1322815679" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DVS->NVS).", "chr_id": "15", "chr_pos": "70668301", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D795", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BZF9-1.793.793", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BZF9-1.801.801", "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": "Q9BZF9-1.966.966", "start_pos": 966, "end_pos": 966, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BZF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "NAEILANYRKGQEEIVTLHA", "down_seq": "IKAQKKELDTIQECIKVKYA", "snv": [ { "evidence": [ { "id": "Q9BZF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BZF9" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "70667788", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E966", "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": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BZF9-1.1065.1065", "start_pos": 1065, "end_pos": 1065, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q9BZF9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] } ], "crossref": [ { "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RDKTVLIEKSHEMERALSRK", "down_seq": "DELNKQLKDLSQKYTEVKNV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ], "site_lbl": "Thr1065" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q9BZF9-1.1074.1074", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BZF9-1.1077.1077", "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": "Q9BZF9-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "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": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q9BZF9", "url": "https://www.iedb.org/epitope/Q9BZF9", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9", "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": "SIQLLCDHGASVNAKDVDGR", "down_seq": "PLVLATQMSRPTICQLLIDR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q9BZF9", "url": "https://www.iedb.org/epitope/Q9BZF9" }, { "database": "iPTMnet", "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr169" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "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": "Q9BZF9-1.434.434", "start_pos": 434, "end_pos": 434, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "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": "Q9BZF9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9", "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": "PAHMQSRSMLRPLELSLPSQ", "down_seq": "SYSENEILKKELEAMRTFCE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr434" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BZF9-1.432.432", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BZF9-1.435.435", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BZF9-1.450.450", "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": "Q9BZF9-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "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": "Q9BZF9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9", "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": "AHMQSRSMLRPLELSLPSQT", "down_seq": "YSENEILKKELEAMRTFCES", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser435" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q9BZF9-1.432.432", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BZF9-1.434.434", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BZF9-1.450.450", "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": "Q9BZF9-1.723.723", "start_pos": 723, "end_pos": 723, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "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": "Q9BZF9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9-1" } ], "reference": [ { "type": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ] } ], "crossref": [ { "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9", "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": "KKITELTLKNQTLQKEIEKV", "down_seq": "LDNKLLKEQAHNLTIEMKNH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" }, { "database": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ], "site_lbl": "Tyr723" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BZF9-1.706.706", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BZF9-1.712.712", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BZF9-1.714.714", "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": "Q9BZF9-1.793.793", "start_pos": 793, "end_pos": 793, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "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": "Q9BZF9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9", "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": "QKYTEKKLEMEKLLLENDSL", "down_seq": "KDVSRLETVFVPPEKHEKEI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser793" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BZF9-1.795.795", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BZF9-1.801.801", "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": "Q9BZF9-1.801.801", "start_pos": 801, "end_pos": 801, "uniprot_canonical_ac": "Q9BZF9-1", "length": 1416, "uniprot_id": "UACA_HUMAN", "protein_name": "Uveal autoantigen with coiled-coil domains and ankyrin repeats", "refseq_ac": "NP_001008225", "refseq_name": "uveal autoantigen with coiled-coil domains and ankyrin repeats isoform 2", "gene_name": "UACA", "gene_names_uniprotkb": "UACA; KIAA1561", "gene_names_refseq": "NUCLING; UACA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BZF9", "url": "https://www.uniprot.org/uniprotkb/Q9BZF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q9BZF9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "Q9BZF9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] } ], "crossref": [ { "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EMEKLLLENDSLSKDVSRLE", "down_seq": "VFVPPEKHEKEIIALKSNIV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BZF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BZF9" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ], "site_lbl": "Thr801" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "706", "end_pos": "706" }, { "start_pos": "712", "end_pos": "712" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1212", "end_pos": "1212" }, { "start_pos": "1225", "end_pos": "1225" }, { "start_pos": "1251", "end_pos": "1251" }, { "start_pos": "1253", "end_pos": "1253" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "567", "end_pos": "567" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1065", "end_pos": "1065" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "801", "end_pos": "801" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BZF9-1.793.793", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BZF9-1.795.795", "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": "Q96PV7-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q96PV7-1", "length": 902, "uniprot_id": "F193B_HUMAN", "protein_name": "Protein FAM193B", "refseq_ac": "NP_001177875", "refseq_name": "protein FAM193B isoform 1", "gene_name": "FAM193B", "gene_names_uniprotkb": "FAM193B; IRIZIO; KIAA1931", "gene_names_refseq": "FAM193B; IRIZIO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" } ], "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": "Q96PV7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96PV7" } ], "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": "Q96PV7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96PV7", "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": "Q96PV7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96PV7" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "773", "end_pos": "773" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "892", "end_pos": "892" } ] } ], "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": "Q96PV7-1.773.773", "start_pos": 773, "end_pos": 773, "uniprot_canonical_ac": "Q96PV7-1", "length": 902, "uniprot_id": "F193B_HUMAN", "protein_name": "Protein FAM193B", "refseq_ac": "NP_001177875", "refseq_name": "protein FAM193B isoform 1", "gene_name": "FAM193B", "gene_names_uniprotkb": "FAM193B; IRIZIO; KIAA1931", "gene_names_refseq": "FAM193B; IRIZIO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QPGRVLELPKVGSCAEAGEG", "down_seq": "RGSRPGPGWAGSPKTEKEKG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" } ], "site_lbl": "Ser773" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "773", "end_pos": "773" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "892", "end_pos": "892" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q96PV7-1.785.785", "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": "Q96PV7-1.785.785", "start_pos": 785, "end_pos": 785, "uniprot_canonical_ac": "Q96PV7-1", "length": 902, "uniprot_id": "F193B_HUMAN", "protein_name": "Protein FAM193B", "refseq_ac": "NP_001177875", "refseq_name": "protein FAM193B isoform 1", "gene_name": "FAM193B", "gene_names_uniprotkb": "FAM193B; IRIZIO; KIAA1931", "gene_names_refseq": "FAM193B; IRIZIO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" } ], "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": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" }, { "database": "iPTMnet", "id": "Q96PV7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96PV7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96PV7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96PV7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SCAEAGEGSRGSRPGPGWAG", "down_seq": "PKTEKEKGSSWRNWPGEAKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q96PV7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96PV7" } ], "site_lbl": "Ser785" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "773", "end_pos": "773" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "892", "end_pos": "892" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q96PV7-1.773.773", "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": "Q96PV7-1.892.892", "start_pos": 892, "end_pos": 892, "uniprot_canonical_ac": "Q96PV7-1", "length": 902, "uniprot_id": "F193B_HUMAN", "protein_name": "Protein FAM193B", "refseq_ac": "NP_001177875", "refseq_name": "protein FAM193B isoform 1", "gene_name": "FAM193B", "gene_names_uniprotkb": "FAM193B; IRIZIO; KIAA1931", "gene_names_refseq": "FAM193B; IRIZIO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" } ], "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": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" }, { "database": "iPTMnet", "id": "Q96PV7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96PV7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96PV7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96PV7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FCLDSAKQTRQKVAVNWTNF", "down_seq": "LKKTTPSTAQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96PV7", "url": "https://www.uniprot.org/uniprotkb/Q96PV7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q96PV7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96PV7" } ], "site_lbl": "Ser892" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "773", "end_pos": "773" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "892", "end_pos": "892" } ] } ], "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": "Q96M60-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAcylation Quantification of Certain Protein by the Proximity Ligation Assay and Clostridium perfringen OGA(D298N)(CpOGA(D298N)).", "journal": "ACS chemical biology", "date": "2021", "authors": "Song J, Liu C, Wang X, Xu B, Liu X, Li Y, Xia J, Li Y, Zhang C, Li D, Sun H", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96M60", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96M60" }, { "database": "O-GlcNAc Atlas", "id": "Q96M60", "url": "https://oglcnac.org/atlas/detail/Q96M60" } ], "reference": [ { "type": "PubMed", "id": "34105348", "url": "https://glygen.org/publication/PubMed/34105348" } ] } ], "crossref": [ { "id": "34105348", "url": "https://glygen.org/publication/PubMed/34105348", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96M60", "url": "https://oglcnac.org/atlas/detail/Q96M60", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs200704844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200704844", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200704844", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200704844", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200704844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200704844", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200704844", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200704844#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200704844", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200704844", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1235994329", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235994329", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1235994329", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1235994329#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1235994329", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235994329", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SGLKPQKGFWIHWKLKELST", "down_seq": "TIHGSKKAPAKSVKERIADS", "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": "Thr311", "evidence": [ { "id": "34105348", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34105348" }, { "id": "Q96M60", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q96M60" } ] } ], "snv": [ { "evidence": [ { "id": "rs200704844", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200704844" }, { "id": "rs200704844", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200704844" }, { "id": "rs200704844", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200704844" }, { "id": "rs200704844", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200704844#frequency_tab" }, { "id": "rs200704844", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200704844" } ], "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": "15", "chr_pos": "49508292", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T311", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1235994329", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235994329" }, { "id": "rs1235994329", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1235994329#frequency_tab" }, { "id": "rs1235994329", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235994329" } ], "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": "15", "chr_pos": "49508291", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T311", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q96M60-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q96M60-1.314.314", "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": "Q96M60-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAcylation Quantification of Certain Protein by the Proximity Ligation Assay and Clostridium perfringen OGA(D298N)(CpOGA(D298N)).", "journal": "ACS chemical biology", "date": "2021", "authors": "Song J, Liu C, Wang X, Xu B, Liu X, Li Y, Xia J, Li Y, Zhang C, Li D, Sun H", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96M60", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96M60" }, { "database": "O-GlcNAc Atlas", "id": "Q96M60", "url": "https://oglcnac.org/atlas/detail/Q96M60" } ], "reference": [ { "type": "PubMed", "id": "34105348", "url": "https://glygen.org/publication/PubMed/34105348" } ] } ], "crossref": [ { "id": "34105348", "url": "https://glygen.org/publication/PubMed/34105348", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96M60", "url": "https://oglcnac.org/atlas/detail/Q96M60", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GLKPQKGFWIHWKLKELSTT", "down_seq": "IHGSKKAPAKSVKERIADSQ", "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": "Thr312", "evidence": [ { "id": "34105348", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34105348" }, { "id": "Q96M60", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q96M60" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q96M60-1.311.311", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96M60-1.314.314", "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": "Q96M60-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAcylation Quantification of Certain Protein by the Proximity Ligation Assay and Clostridium perfringen OGA(D298N)(CpOGA(D298N)).", "journal": "ACS chemical biology", "date": "2021", "authors": "Song J, Liu C, Wang X, Xu B, Liu X, Li Y, Xia J, Li Y, Zhang C, Li D, Sun H", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96M60", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96M60" }, { "database": "O-GlcNAc Atlas", "id": "Q96M60", "url": "https://oglcnac.org/atlas/detail/Q96M60" } ], "reference": [ { "type": "PubMed", "id": "34105348", "url": "https://glygen.org/publication/PubMed/34105348" } ] } ], "crossref": [ { "id": "34105348", "url": "https://glygen.org/publication/PubMed/34105348", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96M60", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96M60", "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": "34105348", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34105348" }, { "id": "Q96M60", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96M60" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "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": "Q96M60-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96M60", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IYPDCLAQAIYATFHEAFPE", "down_seq": "SYLFNDEFKEDLGNNIFLWC", "snv": [ { "evidence": [ { "id": "Q96M60", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60" } ], "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": "15", "chr_pos": "49541745", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S270", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q96M60-1.286.286", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1394380046", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394380046", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1394380046", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394380046", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "AFPESSYLFNDEFKEDLGNN", "down_seq": "FLWCSGLKPQKGFWIHWKLK", "snv": [ { "evidence": [ { "id": "rs1394380046", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394380046" }, { "id": "rs1394380046", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394380046" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNI->NNT).", "chr_id": "15", "chr_pos": "49541697", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I286", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q96M60-1.270.270", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201478342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201478342", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201478342", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201478342", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201478342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201478342", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201478342", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201478342#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "KPQKGFWIHWKLKELSTTTI", "down_seq": "GSKKAPAKSVKERIADSQEH", "snv": [ { "evidence": [ { "id": "rs201478342", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201478342" }, { "id": "rs201478342", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201478342" }, { "id": "rs201478342", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201478342" }, { "id": "rs201478342", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201478342#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HGS->NGS).", "chr_id": "15", "chr_pos": "49508283", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "H314", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q96M60-1.311.311", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96M60-1.312.312", "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": "Q96M60-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96M60", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PAKSVKERIADSQEHISTSI", "down_seq": "FNIIKILNNPRAYTLPISKE", "snv": [ { "evidence": [ { "id": "Q96M60", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "15", "chr_pos": "49371394", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D340", "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:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q96M60-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q96M60-1.350.350", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs949446992", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs949446992", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs949446992", "url": "https://www.ncbi.nlm.nih.gov/snp/rs949446992#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs949446992", "url": "http://gnomad.broadinstitute.org/awesome?query=rs949446992", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "VKERIADSQEHISTSIDFNI", "down_seq": "KILNNPRAYTLPISKEESRL", "snv": [ { "evidence": [ { "id": "rs949446992", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs949446992" }, { "id": "rs949446992", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs949446992#frequency_tab" }, { "id": "rs949446992", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs949446992" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NII->NIT).", "chr_id": "15", "chr_pos": "49371381", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I344", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q96M60-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q96M60-1.350.350", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.350.350", "start_pos": 350, "end_pos": 350, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96M60", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DSQEHISTSIDFNIIKILNN", "down_seq": "RAYTLPISKEESRLSRLATK", "snv": [ { "evidence": [ { "id": "Q96M60", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNT).", "chr_id": "15", "chr_pos": "49371364", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P350", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q96M60-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q96M60-1.344.344", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.374.374", "start_pos": 374, "end_pos": 374, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759641323", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759641323", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759641323", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759641323", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759641323", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759641323", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLPISKEESRLSRLATKSHY", "down_seq": "STGPEFNRVLFNFGGQSPLI", "snv": [ { "evidence": [ { "id": "rs759641323", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759641323" }, { "id": "rs759641323", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759641323" }, { "id": "rs759641323", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759641323" } ], "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": "15", "chr_pos": "49367598", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S374", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.502.502", "start_pos": 502, "end_pos": 502, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2037925014", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037925014", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2037925014", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2037925014#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ECVASLSSSSSSSPSSTDNY", "down_seq": "FEEEEY", "snv": [ { "evidence": [ { "id": "rs2037925014", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037925014" }, { "id": "rs2037925014", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2037925014#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYN->NYS).", "chr_id": "15", "chr_pos": "49328590", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N502", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs149665358", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149665358", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149665358", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149665358", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149665358", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149665358#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149665358", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149665358", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "REIHFRDDDKWSCTLKKIKE", "down_seq": "SSFVSIYTHLWENVPRIFEA", "snv": [ { "evidence": [ { "id": "rs149665358", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149665358" }, { "id": "rs149665358", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149665358" }, { "id": "rs149665358", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149665358#frequency_tab" }, { "id": "rs149665358", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149665358" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "15", "chr_pos": "49589935", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D60", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q96M60-1.75.75", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96M60-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "Q96M60-1", "length": 508, "uniprot_id": "F227B_HUMAN", "protein_name": "Protein FAM227B", "refseq_ac": "NP_001317222", "refseq_name": "protein FAM227B isoform 2", "gene_name": "FAM227B", "gene_names_uniprotkb": "FAM227B; C15orf33", "gene_names_refseq": "C15orf33; FAM227B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96M60", "url": "https://www.uniprot.org/uniprotkb/Q96M60" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96M60", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KKIKEDSSFVSIYTHLWENV", "down_seq": "RIFEALLIMESKLKEYSLIL", "snv": [ { "evidence": [ { "id": "Q96M60", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96M60" } ], "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 (NVP->NVS).", "chr_id": "15", "chr_pos": "49589890", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P75", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "270", "end_pos": "270" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "75", "end_pos": "75" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q96M60-1.60.60", "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": "O94927-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "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": "O94927", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HDDHFGTSYQQWLSSVETLL", "down_seq": "NHPPGHVLAALEHLAAEREA", "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": "Thr236", "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": "O94927", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "19", "chr_pos": "35618080", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T236", "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": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "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": "O94927-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "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": "O94927", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O94927" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O94927", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O94927", "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": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "O94927", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O94927" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "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": "O94927-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1223348302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223348302", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDGLGDTEISRPQAPDQSDS", "down_seq": "QTLPSMVHLIQEGWRTVGVL", "snv": [ { "evidence": [ { "id": "rs1223348302", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223348302" } ], "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": "19", "chr_pos": "35618431", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S284", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94927-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94927", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QEGWRTVGVLVSQRSTLLKE", "down_seq": "QVLTQRLQGLVEEVERRVLG", "snv": [ { "evidence": [ { "id": "O94927", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927" } ], "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": "19", "chr_pos": "35618626", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R315", "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": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94927-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94927", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199765149", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199765149", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199765149", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199765149", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199765149", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199765149", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199765149", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199765149#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199765149", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199765149", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QVLILGLRRCCLWTELKALH", "down_seq": "QSQELQDAAGHRQLLLRELQ", "snv": [ { "evidence": [ { "id": "O94927", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927" }, { "id": "rs199765149", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199765149" }, { "id": "rs199765149", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199765149" }, { "id": "rs199765149", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199765149" }, { "id": "rs199765149", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199765149#frequency_tab" }, { "id": "rs199765149", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199765149" } ], "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 (DQS->NQS).", "chr_id": "19", "chr_pos": "35618948", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D360", "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": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94927-1.401.401", "start_pos": 401, "end_pos": 401, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94927", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AKQQRILHWRQLVEETQEQV", "down_seq": "LLIKGNSASKTRLCRSPGEV", "snv": [ { "evidence": [ { "id": "O94927", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "35619446", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R401", "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:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "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": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94927-1.448.448", "start_pos": 448, "end_pos": 448, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94927", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KVVPTFEAVAPQSRELLRCL", "down_seq": "EEVRHLPHILLGTLLRHRPG", "snv": [ { "evidence": [ { "id": "O94927", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "19", "chr_pos": "35619694", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E448", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "O94927-1.486.486", "start_pos": 486, "end_pos": 486, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94927", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RPGELKPLPTVLPSIHQLHP", "down_seq": "SPRGSSFIALSHKLGLPPGK", "snv": [ { "evidence": [ { "id": "O94927", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94927" } ], "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": "19", "chr_pos": "35620062", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A486", "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": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94927-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780365704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780365704", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780365704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780365704", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780365704", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780365704#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780365704", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780365704", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RRKLELEAAVTRLRAEIQEL", "down_seq": "QSLELMERDTEAQDTAMEQA", "snv": [ { "evidence": [ { "id": "rs780365704", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780365704" }, { "id": "rs780365704", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780365704" }, { "id": "rs780365704", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780365704#frequency_tab" }, { "id": "rs780365704", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780365704" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DQS->NQS).", "chr_id": "19", "chr_pos": "35615105", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D95", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94927-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "O94927-1", "length": 633, "uniprot_id": "HAUS5_HUMAN", "protein_name": "HAUS augmin-like complex subunit 5", "refseq_ac": "NP_056117", "refseq_name": "HAUS augmin-like complex subunit 5", "gene_name": "HAUS5", "gene_names_uniprotkb": "HAUS5; KIAA0841", "gene_names_refseq": "HAUS5; KIAA0841; dgt5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" } ], "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": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" }, { "database": "iPTMnet", "id": "O94927", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94927" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O94927", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94927", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HSQRTVKKIRGNLLWYGHQD", "down_seq": "PQVRRKLELEAAVTRLRAEI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O94927", "url": "https://www.uniprot.org/uniprotkb/O94927" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O94927", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94927" } ], "site_lbl": "Ser71" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "236", "end_pos": "236" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "95", "end_pos": "95" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHX9-1.611.611", "start_pos": 611, "end_pos": 611, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs748313894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748313894", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748313894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748313894", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748313894", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748313894", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YVFAIIGINLFRGVIVALPG", "down_seq": "SSLAPANGSAPCGSFEQLEY", "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": "Asn611", "evidence": [ { "id": "Q8NHX9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs748313894", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748313894" }, { "id": "rs748313894", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748313894" }, { "id": "rs748313894", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748313894" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->SSS).", "chr_id": "11", "chr_pos": "69085280", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N611", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8NHX9-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHX9-1.613.613", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHX9-1.618.618", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHX9-1.620.620", "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": "Q8NHX9-1.618.618", "start_pos": 618, "end_pos": 618, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs565376754", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565376754", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs565376754", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs565376754", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs565376754", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565376754", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs565376754", "url": "http://gnomad.broadinstitute.org/awesome?query=rs565376754", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs149949063", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149949063", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149949063", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149949063", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs149949063", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149949063", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149949063", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149949063#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149949063", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149949063", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "INLFRGVIVALPGNSSLAPA", "down_seq": "GSAPCGSFEQLEYWANNFDD", "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": "Asn618", "evidence": [ { "id": "Q8NHX9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs565376754", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565376754" }, { "id": "rs565376754", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs565376754" }, { "id": "rs565376754", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565376754" }, { "id": "rs565376754", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs565376754" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGS->DGS).", "chr_id": "11", "chr_pos": "69085684", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N618", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NGS->KGS).", "chr_id": "11", "chr_pos": "69085686", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "N618", "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": "rs149949063", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149949063" }, { "id": "rs149949063", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149949063" }, { "id": "rs149949063", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149949063" }, { "id": "rs149949063", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149949063#frequency_tab" }, { "id": "rs149949063", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149949063" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGS->SGS).", "chr_id": "11", "chr_pos": "69085685", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N618", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHX9-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHX9-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHX9-1.613.613", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHX9-1.620.620", "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": 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": "Q8NHX9-1.11.12", "start_pos": 11, "end_pos": 12, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Convergent regulation of the lysosomal two-pore channel-2 by Mg(2)(+), NAADP, PI(3,5)P(2) and multiple protein kinases.", "journal": "The EMBO journal", "date": "2014", "authors": "Jha A, Ahuja M, Patel S, Brailoiu E, Muallem S", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "reference": [ { "type": "PubMed", "id": "24502975", "url": "https://glygen.org/publication/PubMed/24502975" } ] }, { "title": "An NAADP-gated two-pore channel targeted to the plasma membrane uncouples triggering from amplifying Ca2+ signals.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Brailoiu E, Rahman T, Churamani D, Prole DL, Brailoiu GC, Hooper R, Taylor CW, Patel S", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "reference": [ { "type": "PubMed", "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24502975", "url": "https://glygen.org/publication/PubMed/24502975", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "LL", "start_aa": "L", "up_seq": "MAEPQAESEP", "down_seq": "GGARGGGGDWPAGLTTYRSI", "mutagenesis": [ { "sequence_org": "LL", "sequence_mut": "AA", "comment": "Localizes at the plasma membrane.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "24502975", "url": "https://glygen.org/publication/PubMed/24502975" }, { "database": "PubMed", "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "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": "Q8NHX9-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of phospholipid activation of the human TPC2 channel.", "journal": "eLife", "date": "2019", "authors": "She J, Zeng W, Guo J, Chen Q, Bai XC, Jiang Y", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "RefSeq", "id": "NP_620714", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_620714" } ], "reference": [ { "type": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs767658519", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767658519", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767658519", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767658519", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767658519", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767658519", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PLRIRRLLRPFFLLQNSSMM", "down_seq": "KTLKCIRWSLPEMASVGLLL", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Strongly reduces binding with phosphatidylinositol 3,5-bisphosphate.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "snv": [ { "evidence": [ { "id": "rs767658519", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767658519" }, { "id": "rs767658519", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767658519" }, { "id": "rs767658519", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767658519" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KKT->NKT).", "chr_id": "11", "chr_pos": "69062946", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K203", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8NHX9-1.204.204", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHX9-1.207.207", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q8NHX9-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of phospholipid activation of the human TPC2 channel.", "journal": "eLife", "date": "2019", "authors": "She J, Zeng W, Guo J, Chen Q, Bai XC, Jiang Y", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "RefSeq", "id": "NP_620714", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_620714" } ], "reference": [ { "type": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] }, { "title": "Agonist-mediated switching of ion selectivity in TPC2 differentially promotes lysosomal function.", "journal": "eLife", "date": "2020", "authors": "Gerndt S, Chen CC, Chao YK, Yuan Y, Burgstaller S, Scotto Rosato A, Krogsaeter E, Urban N, Jacob K, Nguyen ONP, Miller MT, Keller M, Vollmar AM, Gudermann T, Zierler S, Schredelseker J, Schaefer M, Biel M, Malli R, Wahl-Schott C, Bracher F, Patel S, Grimm C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "reference": [ { "type": "PubMed", "id": "32167471", "url": "https://glygen.org/publication/PubMed/32167471" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32167471", "url": "https://glygen.org/publication/PubMed/32167471", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LRIRRLLRPFFLLQNSSMMK", "down_seq": "TLKCIRWSLPEMASVGLLLA", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Strongly reduces binding with phosphatidylinositol 3,5-bisphosphate. Decreases sodium transport. No effect on calcium release.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" }, { "database": "PubMed", "id": "32167471", "url": "https://glygen.org/publication/PubMed/32167471" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8NHX9-1.203.203", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHX9-1.207.207", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHX9-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of phospholipid activation of the human TPC2 channel.", "journal": "eLife", "date": "2019", "authors": "She J, Zeng W, Guo J, Chen Q, Bai XC, Jiang Y", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "RefSeq", "id": "NP_620714", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_620714" } ], "reference": [ { "type": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RRLLRPFFLLQNSSMMKKTL", "down_seq": "CIRWSLPEMASVGLLLAIHL", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Reduces binding with phosphatidylinositol 3,5-bisphosphate.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8NHX9-1.203.203", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHX9-1.204.204", "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": "Q8NHX9-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Ebola virus. Two-pore channels control Ebola virus host cell entry and are drug targets for disease treatment.", "journal": "Science (New York, N.Y.)", "date": "2015", "authors": "Sakurai Y, Kolokoltsov AA, Chen CC, Tidwell MW, Bauta WE, Klugbauer N, Grimm C, Wahl-Schott C, Biel M, Davey RA", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "reference": [ { "type": "PubMed", "id": "25722412", "url": "https://glygen.org/publication/PubMed/25722412" } ] }, { "title": "An NAADP-gated two-pore channel targeted to the plasma membrane uncouples triggering from amplifying Ca2+ signals.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Brailoiu E, Rahman T, Churamani D, Prole DL, Brailoiu GC, Hooper R, Taylor CW, Patel S", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "reference": [ { "type": "PubMed", "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25722412", "url": "https://glygen.org/publication/PubMed/25722412", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "DGQDRERLTYFQNLPESLTS", "down_seq": "LVLLTTANNPDVMIPAYSKN", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "P", "comment": "No effect on lysosomal location. Loss of NAADP-sensitive calcium-release channel activity. Inhibits Ebola virus infection.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "25722412", "url": "https://glygen.org/publication/PubMed/25722412" }, { "database": "PubMed", "id": "20880839", "url": "https://glygen.org/publication/PubMed/20880839" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NHX9-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHX9-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHX9-1.276.276", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHX9-1.276.276", "start_pos": 276, "end_pos": 276, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "TPC proteins are phosphoinositide- activated sodium-selective ion channels in endosomes and lysosomes.", "journal": "Cell", "date": "2012", "authors": "Wang X, Zhang X, Dong XP, Samie M, Li X, Cheng X, Goschka A, Shen D, Zhou Y, Harlow J, Zhu MX, Clapham DE, Ren D, Xu H", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "reference": [ { "type": "PubMed", "id": "23063126", "url": "https://glygen.org/publication/PubMed/23063126" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23063126", "url": "https://glygen.org/publication/PubMed/23063126", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QNLPESLTSLLVLLTTANNP", "down_seq": "VMIPAYSKNRAYAIFFIVFT", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "K", "comment": "Not activated by phosphatidylinositol 3,5-bisphosphate.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "23063126", "url": "https://glygen.org/publication/PubMed/23063126" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHX9-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NHX9-1.265.265", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHX9-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHX9-1.287.287", "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": "Q8NHX9-1.322.322", "start_pos": 322, "end_pos": 322, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of phospholipid activation of the human TPC2 channel.", "journal": "eLife", "date": "2019", "authors": "She J, Zeng W, Guo J, Chen Q, Bai XC, Jiang Y", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "RefSeq", "id": "NP_620714", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_620714" } ], "reference": [ { "type": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FLMNLLTAIIYSQFRGYLMK", "down_seq": "LQTSLFRRRLGTRAAFEVLS", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Reduces binding with phosphatidylinositol 3,5-bisphosphate.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q8NHX9-1.329.329", "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": "Q8NHX9-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of phospholipid activation of the human TPC2 channel.", "journal": "eLife", "date": "2019", "authors": "She J, Zeng W, Guo J, Chen Q, Bai XC, Jiang Y", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "RefSeq", "id": "NP_620714", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_620714" } ], "reference": [ { "type": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AIIYSQFRGYLMKSLQTSLF", "down_seq": "RRLGTRAAFEVLSSMVGEGG", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Reduces binding with phosphatidylinositol 3,5-bisphosphate.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8NHX9-1.322.322", "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": "Q8NHX9-1.551.551", "start_pos": 551, "end_pos": 551, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of phospholipid activation of the human TPC2 channel.", "journal": "eLife", "date": "2019", "authors": "She J, Zeng W, Guo J, Chen Q, Bai XC, Jiang Y", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "RefSeq", "id": "NP_620714", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_620714" } ], "reference": [ { "type": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RPEMVGLLSLWDMTRMLNML", "down_seq": "VFRFLRIIPSMKLMAVVAST", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "R", "comment": "Requires both phosphatidylinositol 3,5-bisphosphate and a positive membrane potential for activation.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" }, { "database": "PubMed", "id": "30860481", "url": "https://glygen.org/publication/PubMed/30860481" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "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": "Q8NHX9-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746923249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746923249", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746923249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746923249", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746923249", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746923249#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746923249", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746923249", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LSFTIFLILFLAFIETPSSL", "down_seq": "STADVRYRAAPWEPPCGLTE", "snv": [ { "evidence": [ { "id": "rs746923249", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746923249" }, { "id": "rs746923249", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746923249" }, { "id": "rs746923249", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746923249#frequency_tab" }, { "id": "rs746923249", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746923249" } ], "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 (TST->NST).", "chr_id": "11", "chr_pos": "69055240", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T106", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q8NHX9-1.125.125", "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": "Q8NHX9-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LTSTADVRYRAAPWEPPCGL", "down_seq": "ESVEVLCLLVFAADLSVKGY", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "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 (TES->NES).", "chr_id": "11", "chr_pos": "69055297", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T125", "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": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHX9-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHX9-1.139.139", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs772440038", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772440038", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772440038", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772440038", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772440038", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772440038#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772440038", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772440038", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EPPCGLTESVEVLCLLVFAA", "down_seq": "LSVKGYLFGWAHFQKNLWLL", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" }, { "id": "rs772440038", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772440038" }, { "id": "rs772440038", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772440038" }, { "id": "rs772440038", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772440038#frequency_tab" }, { "id": "rs772440038", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772440038" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "11", "chr_pos": "69055338", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D139", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8NHX9-1.125.125", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2134530487", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2134530487", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2134530487", "url": "https://www.ensembl.org/id/rs2134530487", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2134530487", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2134530487", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HFQKNLWLLGYLVVLVVSLV", "down_seq": "WTVSLSLVCHEPLRIRRLLR", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" }, { "id": "rs2134530487", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2134530487" }, { "id": "rs2134530487", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2134530487" }, { "id": "rs2134530487", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2134530487" } ], "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 (DWT->NWT).", "chr_id": "11", "chr_pos": "69057659", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D171", "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": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.259.259", "start_pos": 259, "end_pos": 259, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763092453", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763092453", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763092453", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763092453", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AGGKQDDGQDRERLTYFQNL", "down_seq": "ESLTSLLVLLTTANNPDVMI", "snv": [ { "evidence": [ { "id": "rs763092453", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763092453" }, { "id": "rs763092453", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763092453" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLP->NLT).", "chr_id": "11", "chr_pos": "69067551", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P259", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8NHX9-1.265.265", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHX9-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHX9-1.276.276", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LTYFQNLPESLTSLLVLLTT", "down_seq": "NNPDVMIPAYSKNRAYAIFF", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "69067590", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A272", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8NHX9-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHX9-1.265.265", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHX9-1.276.276", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHX9-1.287.287", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1007252609", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1007252609", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1007252609", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1007252609", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VLLTTANNPDVMIPAYSKNR", "down_seq": "YAIFFIVFTVIGSLFLMNLL", "snv": [ { "evidence": [ { "id": "rs1007252609", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1007252609" }, { "id": "rs1007252609", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1007252609" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRA->NRS).", "chr_id": "11", "chr_pos": "69070459", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A287", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1007252609", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1007252609" }, { "id": "rs1007252609", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1007252609" } ], "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": "69070459", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A287", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHX9-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NHX9-1.276.276", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHX9-1.297.297", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "Q8NHX9-1.297.297", "start_pos": 297, "end_pos": 297, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VMIPAYSKNRAYAIFFIVFT", "down_seq": "IGSLFLMNLLTAIIYSQFRG", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "V", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "11", "chr_pos": "69070489", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V297", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8NHX9-1.287.287", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q8NHX9-1.372.372", "start_pos": 372, "end_pos": 372, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs756906978", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756906978", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756906978", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756906978", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756906978", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756906978#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756906978", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756906978", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PQAVGVKPQNLLQVLQKVQL", "down_seq": "SSHKQAMMEKVRSYGSVLLS", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" }, { "id": "rs756906978", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756906978" }, { "id": "rs756906978", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756906978" }, { "id": "rs756906978", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756906978#frequency_tab" }, { "id": "rs756906978", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756906978" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "11", "chr_pos": "69072679", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D372", "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": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8NHX9-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHX9-1.384.384", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.376.376", "start_pos": 376, "end_pos": 376, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GVKPQNLLQVLQKVQLDSSH", "down_seq": "QAMMEKVRSYGSVLLSAEEF", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "69072692", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K376", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8NHX9-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHX9-1.384.384", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.384.384", "start_pos": 384, "end_pos": 384, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QVLQKVQLDSSHKQAMMEKV", "down_seq": "SYGSVLLSAEEFQKLFNELD", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "69072921", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R384", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID: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": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHX9-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NHX9-1.376.376", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ANLVSICVFLVLDADVLPAE", "down_seq": "DDFILGILNCVFIVYYLLEM", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "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": "11", "chr_pos": "69078773", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R464", "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": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.504.504", "start_pos": 504, "end_pos": 504, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1855899683", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1855899683", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1855899683", "url": "https://www.ensembl.org/id/rs1855899683", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MLLKVFALGLRGYLSYPSNV", "down_seq": "DGLLTVVLLVLEISTLAVYR", "snv": [ { "evidence": [ { "id": "rs1855899683", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1855899683" }, { "id": "rs1855899683", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1855899683" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVF->NVS).", "chr_id": "11", "chr_pos": "69078992", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F504", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.572.572", "start_pos": 572, "end_pos": 572, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VFRFLRIIPSMKLMAVVAST", "down_seq": "LGLVQNMRAFGGILVVVYYV", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "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 (4).", "chr_id": "11", "chr_pos": "69083969", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V572", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8NHX9-1.580.580", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.580.580", "start_pos": 580, "end_pos": 580, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1360401958", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360401958", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1360401958", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1360401958#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1360401958", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360401958", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1360401958", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1360401958", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PSMKLMAVVASTVLGLVQNM", "down_seq": "AFGGILVVVYYVFAIIGINL", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" }, { "id": "rs1360401958", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360401958" }, { "id": "rs1360401958", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1360401958#frequency_tab" }, { "id": "rs1360401958", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360401958" }, { "id": "rs1360401958", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1360401958" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NMR->NMC).", "chr_id": "11", "chr_pos": "69083993", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R580", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NHX9-1.572.572", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.601.601", "start_pos": 601, "end_pos": 601, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764962459", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764962459", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764962459", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764962459", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764962459", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764962459", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "AFGGILVVVYYVFAIIGINL", "down_seq": "RGVIVALPGNSSLAPANGSA", "snv": [ { "evidence": [ { "id": "rs764962459", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764962459" }, { "id": "rs764962459", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764962459" }, { "id": "rs764962459", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764962459" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLF->NLC).", "chr_id": "11", "chr_pos": "69085250", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F601", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q8NHX9-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHX9-1.613.613", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHX9-1.618.618", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHX9-1.620.620", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.613.613", "start_pos": 613, "end_pos": 613, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FAIIGINLFRGVIVALPGNS", "down_seq": "LAPANGSAPCGSFEQLEYWA", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSN).", "chr_id": "11", "chr_pos": "69085286", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S613", "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": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHX9-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHX9-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHX9-1.618.618", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHX9-1.620.620", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.620.620", "start_pos": 620, "end_pos": 620, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1289667112", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289667112", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1289667112", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1289667112", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200514919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514919", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200514919", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200514919", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200514919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514919", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200514919", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200514919#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200514919", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200514919", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LFRGVIVALPGNSSLAPANG", "down_seq": "APCGSFEQLEYWANNFDDFA", "snv": [ { "evidence": [ { "id": "rs1289667112", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289667112" }, { "id": "rs1289667112", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1289667112" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGS->NGA).", "chr_id": "11", "chr_pos": "69085690", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S620", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200514919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514919" }, { "id": "rs200514919", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200514919" }, { "id": "rs200514919", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514919" }, { "id": "rs200514919", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200514919#frequency_tab" }, { "id": "rs200514919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200514919" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGS->NGL).", "chr_id": "11", "chr_pos": "69085691", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00117739", "site_lbl": "S620", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200514919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514919" }, { "id": "rs200514919", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200514919" }, { "id": "rs200514919", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514919" }, { "id": "rs200514919", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200514919#frequency_tab" }, { "id": "rs200514919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200514919" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGS->NGW).", "chr_id": "11", "chr_pos": "69085691", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.00117739", "site_lbl": "S620", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHX9-1.601.601", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NHX9-1.611.611", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHX9-1.613.613", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHX9-1.618.618", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "Q8NHX9-1.655.655", "start_pos": 655, "end_pos": 655, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1167531560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1167531560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1167531560", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1167531560", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "NFDDFAAALVTLWNLMVVNN", "down_seq": "QVFLDAYRRYSGPWSKIYFV", "snv": [ { "evidence": [ { "id": "rs1167531560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1167531560" }, { "id": "rs1167531560", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1167531560" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNW->NNC).", "chr_id": "11", "chr_pos": "69085892", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W655", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q8NHX9-1.666.666", "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": "Q8NHX9-1.704.704", "start_pos": 704, "end_pos": 704, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IWVNLFLALILENFLHKWDP", "down_seq": "SHLQPLAGTPEATYQMTVEL", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "69087137", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R704", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHX9-1.734.734", "start_pos": 734, "end_pos": 734, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PEATYQMTVELLFRDILEEP", "down_seq": "EDELTERLSQHPHLWLCR", "snv": [ { "evidence": [ { "id": "Q8NHX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHX9" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "11", "chr_pos": "69087895", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G734", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q8NHX9-1.666.666", "start_pos": 666, "end_pos": 666, "uniprot_canonical_ac": "Q8NHX9-1", "length": 752, "uniprot_id": "TPC2_HUMAN", "protein_name": "Two pore channel protein 2", "refseq_ac": "NP_620714", "refseq_name": "two pore channel protein 2", "gene_name": "TPCN2", "gene_names_uniprotkb": "TPCN2; TPC2", "gene_names_refseq": "SHEP10; TPC2; TPCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHX9", "url": "https://www.uniprot.org/uniprotkb/Q8NHX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Characterization of Two-Pore Channel 2 by Nuclear Membrane Electrophysiology.", "journal": "Scientific reports", "date": "2016", "authors": "Lee CS, Tong BC, Cheng CW, Hung HC, Cheung KH", "evidence": [ { "database": "iPTMnet", "id": "Q8NHX9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHX9" } ], "reference": [ { "type": "PubMed", "id": "26838264", "url": "https://glygen.org/publication/PubMed/26838264" } ] } ], "crossref": [ { "id": "Q8NHX9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHX9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "26838264", "url": "https://glygen.org/publication/PubMed/26838264", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LWNLMVVNNWQVFLDAYRRY", "down_seq": "GPWSKIYFVLWWLVSSVIWV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHX9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHX9" }, { "database": "PubMed", "id": "26838264", "url": "https://glygen.org/publication/PubMed/26838264" } ], "site_lbl": "Ser666" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "611", "end_pos": "611" }, { "start_pos": "618", "end_pos": "618" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "12" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "551", "end_pos": "551" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "572", "end_pos": "572" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "734", "end_pos": "734" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "666", "end_pos": "666" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NHX9-1.655.655", "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": "Q9Y3B2-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9Y3B2-1", "length": 195, "uniprot_id": "EXOS1_HUMAN", "protein_name": "Exosome complex component CSL4", "refseq_ac": "NP_001305291", "refseq_name": "exosome complex component CSL4 isoform b", "gene_name": "EXOSC1", "gene_names_uniprotkb": "EXOSC1; CGI-108; CSL4", "gene_names_refseq": "CGI-108; CSL4; Csl4p; EXOSC1; PCH1F; SKI4; Ski4p; p13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" } ], "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": "Q9Y3B2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9Y3B2" } ], "reference": [ { "type": "PubMed", "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054" } ] }, { "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": "Q9Y3B2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9Y3B2" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] }, { "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": "Q9Y3B2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9Y3B2" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "crossref": [ { "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9Y3B2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9Y3B2", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "34229054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34229054" }, { "id": "Q9Y3B2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9Y3B2" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "191", "end_pos": "191" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "21", "end_pos": "21" }, { "start_pos": "98", "end_pos": "98" } ] } ], "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": "Q9Y3B2-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "Q9Y3B2-1", "length": 195, "uniprot_id": "EXOS1_HUMAN", "protein_name": "Exosome complex component CSL4", "refseq_ac": "NP_001305291", "refseq_name": "exosome complex component CSL4 isoform b", "gene_name": "EXOSC1", "gene_names_uniprotkb": "EXOSC1; CGI-108; CSL4", "gene_names_refseq": "CGI-108; CSL4; Csl4p; EXOSC1; PCH1F; SKI4; Ski4p; p13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y3B2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y3B2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "EMQCPKTHTKEFRKVARVQP", "down_seq": "FLQT", "snv": [ { "evidence": [ { "id": "Q9Y3B2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y3B2" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "10", "chr_pos": "97436462", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E191", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "191", "end_pos": "191" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "21", "end_pos": "21" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9Y3B2-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "Q9Y3B2-1", "length": 195, "uniprot_id": "EXOS1_HUMAN", "protein_name": "Exosome complex component CSL4", "refseq_ac": "NP_001305291", "refseq_name": "exosome complex component CSL4 isoform b", "gene_name": "EXOSC1", "gene_names_uniprotkb": "EXOSC1; CGI-108; CSL4", "gene_names_refseq": "CGI-108; CSL4; Csl4p; EXOSC1; PCH1F; SKI4; Ski4p; p13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" } ], "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": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" }, { "database": "iPTMnet", "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" }, { "database": "iPTMnet", "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2" } ], "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": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" }, { "database": "iPTMnet", "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" }, { "database": "iPTMnet", "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MAPPVRYCIPGERLCNLEEG", "down_seq": "PGSGTYTRHGYIFSSLAGCL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2" } ], "site_lbl": "Ser21" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "191", "end_pos": "191" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "21", "end_pos": "21" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9Y3B2-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "Q9Y3B2-1", "length": 195, "uniprot_id": "EXOS1_HUMAN", "protein_name": "Exosome complex component CSL4", "refseq_ac": "NP_001305291", "refseq_name": "exosome complex component CSL4 isoform b", "gene_name": "EXOSC1", "gene_names_uniprotkb": "EXOSC1; CGI-108; CSL4", "gene_names_refseq": "CGI-108; CSL4; Csl4p; EXOSC1; PCH1F; SKI4; Ski4p; p13", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" } ], "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": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" }, { "database": "iPTMnet", "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "INSRFAKVHILYVGSMPLKN", "down_seq": "FRGTIRKEDVRATEKDKVEI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9Y3B2", "url": "https://www.uniprot.org/uniprotkb/Q9Y3B2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9Y3B2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y3B2" } ], "site_lbl": "Ser98" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "191", "end_pos": "191" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "21", "end_pos": "21" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEV8-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification.", "journal": "Talanta", "date": "2017", "authors": "Shen B, Zhang W, Shi Z, Tian F, Deng Y, Sun C, Wang G, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEV8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEV8", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811", "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": "Q8NEV8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEV8" }, { "id": "28411811", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28411811" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "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": "Q8NEV8-1.1292.1292", "start_pos": 1292, "end_pos": 1292, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TQNTNLLIESPQVETETFPN", "down_seq": "LEKDKQNYSTREQSGTPSCE", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "108511633", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1292", "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: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": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEV8-1.1450.1450", "start_pos": 1450, "end_pos": 1450, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSEVNIGNSQTRRSSWECTG", "down_seq": "GRAIPFTGSGKCPQKDHTST", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "108511158", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1450", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEV8-1.1543.1543", "start_pos": 1543, "end_pos": 1543, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TQSDEPNLESLQSEPRELPQ", "down_seq": "SQEANMTESRKAEDEMQKSA", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "108510879", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1543", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEV8-1.1698.1698", "start_pos": 1698, "end_pos": 1698, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LPNREPSTHVSNQKSNSISQ", "down_seq": "HQNEFKNVSESPSKHENSKD", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "108510414", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1698", "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:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q8NEV8-1.1707.1707", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NEV8-1.1716.1716", "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": "Q8NEV8-1.320.320", "start_pos": 320, "end_pos": 320, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TREPRVFKEDYVQKNTFGST", "down_seq": "LCFDSRQRSALPATGHFTAR", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "108514548", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S320", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEV8-1.592.592", "start_pos": 592, "end_pos": 592, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "QLTPHFGTPNVCSMTGSSYH", "down_seq": "KSSELVSQQDSSPVEVHINK", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "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": "11", "chr_pos": "108513733", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V592", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q8NEV8-1.603.603", "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": "Q8NEV8-1.676.676", "start_pos": 676, "end_pos": 676, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IFPNKPASHPMRSHTEVTVT", "down_seq": "SNSVDSLPLAKSQPNILVTE", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "14", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: patient count (14/4799).", "chr_id": "11", "chr_pos": "108513480", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S676", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEV8-1.853.853", "start_pos": 853, "end_pos": 853, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEV8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LTVNNEDISRIITNNHWSSA", "down_seq": "TDTQNAQYSKCKLTPGHKTS", "snv": [ { "evidence": [ { "id": "Q8NEV8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEV8" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "108512949", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L853", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID: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": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEV8-1.1028.1028", "start_pos": 1028, "end_pos": 1028, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNSKVSELDTIYCTLPRKSS", "down_seq": "FLIHGRQSGSKIMAASLRNG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1028" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "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": "Q8NEV8-1.1086.1086", "start_pos": 1086, "end_pos": 1086, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLNKFSPSSPESANECSKVL", "down_seq": "DSALEAPEATERMTNVKSSG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1086" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "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": "Q8NEV8-1.1124.1124", "start_pos": 1124, "end_pos": 1124, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSGSTSVRKGPLPFLINRAM", "down_seq": "CPSGEPHASTGREGRKKPLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1124" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "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": "Q8NEV8-1.1505.1505", "start_pos": 1505, "end_pos": 1505, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RGDIGTNCQKMTNKTLSHSE", "down_seq": "QVFALTPALHKLQLGEETQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1505" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8NEV8-1.1511.1511", "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": "Q8NEV8-1.1511.1511", "start_pos": 1511, "end_pos": 1511, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.", "journal": "Immunity", "date": "2017-02-21", "authors": "Abelin Jennifer G, Keskin Derin B, Sarkizova Siranush, Hartigan Christina R, Zhang Wandi, Sidney John, Stevens Jonathan, Lane William, Zhang Guang Lan, Eisenhaure Thomas M, Clauser Karl R, Hacohen Nir, Rooney Michael S, Carr Steven A, Wu Catherine J", "evidence": [ { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "28228285", "url": "https://glygen.org/publication/PubMed/28228285" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.iedb.org/epitope/Q8NEV8", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "28228285", "url": "https://glygen.org/publication/PubMed/28228285", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NCQKMTNKTLSHSESQVFAL", "down_seq": "PALHKLQLGEETQSDEPNLE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q8NEV8", "url": "https://www.iedb.org/epitope/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" }, { "database": "PubMed", "id": "28228285", "url": "https://glygen.org/publication/PubMed/28228285" } ], "site_lbl": "Thr1511" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NEV8-1.1505.1505", "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": "Q8NEV8-1.1602.1602", "start_pos": 1602, "end_pos": 1602, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "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": "LVKGENRSSVKHRLAAMSKA", "down_seq": "RKFPAKDVSPRRHVATIFPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser1602" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "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": "Q8NEV8-1.1707.1707", "start_pos": 1707, "end_pos": 1707, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q8NEV8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSNQKSNSISQRHQNEFKNV", "down_seq": "ESPSKHENSKDVTAAQNLVR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ], "site_lbl": "Ser1707" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8NEV8-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NEV8-1.1716.1716", "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": "Q8NEV8-1.1716.1716", "start_pos": 1716, "end_pos": 1716, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q8NEV8-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQRHQNEFKNVSESPSKHEN", "down_seq": "KDVTAAQNLVRESGAPSPIT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ], "site_lbl": "Ser1716" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NEV8-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NEV8-1.1707.1707", "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": "Q8NEV8-1.1753.1753", "start_pos": 1753, "end_pos": 1753, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPITFTSLREAEFSDNQRRL", "down_seq": "PPFPLEPAQKSRVSSPLASF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1753" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q8NEV8-1.1768.1768", "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": "Q8NEV8-1.1768.1768", "start_pos": 1768, "end_pos": 1768, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NQRRLSPPFPLEPAQKSRVS", "down_seq": "PLASFLQQQRSASSLEWEPE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1768" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NEV8-1.1753.1753", "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": "Q8NEV8-1.1821.1821", "start_pos": 1821, "end_pos": 1821, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NVHGDLLRKSHPPKVRERHF", "down_seq": "ESTSIDNALSRLTLGNEFSV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1821" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "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": "Q8NEV8-1.1851.1851", "start_pos": 1851, "end_pos": 1851, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRLTLGNEFSVNNGYSRRFR", "down_seq": "FSELPSCDGNESWAYRSGTK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser1851" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "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": "Q8NEV8-1.603.603", "start_pos": 603, "end_pos": 603, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CSMTGSSYHVKSSELVSQQD", "down_seq": "SPVEVHINKEASSFGIAQTL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser603" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NEV8-1.592.592", "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": "Q8NEV8-1.806.806", "start_pos": 806, "end_pos": 806, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TDKSNDIKQDKRFTENRKLG", "down_seq": "TASLPFIQEHRTPPSFPRTD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser806" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8NEV8-1.809.809", "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": "Q8NEV8-1.809.809", "start_pos": 809, "end_pos": 809, "uniprot_canonical_ac": "Q8NEV8-1", "length": 1989, "uniprot_id": "EXPH5_HUMAN", "protein_name": "Exophilin-5", "refseq_ac": "NP_001294948", "refseq_name": "exophilin-5 isoform 2", "gene_name": "EXPH5", "gene_names_uniprotkb": "EXPH5; KIAA0624; SLAC2B", "gene_names_refseq": "EBS4; EXPH5; SLAC2-B; SLAC2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" } ], "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": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNDIKQDKRFTENRKLGSTA", "down_seq": "LPFIQEHRTPPSFPRTDQGC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEV8", "url": "https://www.uniprot.org/uniprotkb/Q8NEV8" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEV8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEV8" } ], "site_lbl": "Ser809" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1450", "end_pos": "1450" }, { "start_pos": "1543", "end_pos": "1543" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "592", "end_pos": "592" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "853", "end_pos": "853" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1028", "end_pos": "1028" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1505", "end_pos": "1505" }, { "start_pos": "1511", "end_pos": "1511" }, { "start_pos": "1602", "end_pos": "1602" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1716", "end_pos": "1716" }, { "start_pos": "1753", "end_pos": "1753" }, { "start_pos": "1768", "end_pos": "1768" }, { "start_pos": "1821", "end_pos": "1821" }, { "start_pos": "1851", "end_pos": "1851" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "809", "end_pos": "809" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8NEV8-1.806.806", "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": "Q8IYU2-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MERAMEQLNR", "down_seq": "TRSLRRARTVELPEDNETAV", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "Exists as a mixture of monomer and dimer; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] }, { "sequence_org": "L", "sequence_mut": "D", "comment": "Monomeric; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8IYU2-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IYU2-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IYU2-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IYU2-1.20.20", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IYU2-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "YSADVNICNNEGLTAIHWLA", "down_seq": "NGRTELLHDLVQHVSDVDVE", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "A", "comment": "Promotes ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "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": "Q8IYU2-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MERAMEQLNRLTR", "down_seq": "LRRARTVELPEDNETAVYTL", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "E", "comment": "Monomeric; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IYU2-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IYU2-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IYU2-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IYU2-1.20.20", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IYU2-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MERAMEQLNRLTRS", "down_seq": "RRARTVELPEDNETAVYTLM", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "Monomeric; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] }, { "sequence_org": "L", "sequence_mut": "D", "comment": "Monomeric; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8IYU2-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IYU2-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IYU2-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IYU2-1.20.20", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IYU2-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "HVSDVDVEDAMGQTALHVAC", "down_seq": "NGHKTTVQCLLDSGADINRP", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Impairs ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8IYU2-1.174.174", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IYU2-1.175.175", "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": "Q8IYU2-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VSDVDVEDAMGQTALHVACQ", "down_seq": "GHKTTVQCLLDSGADINRPN", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Impairs ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8IYU2-1.173.173", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IYU2-1.175.175", "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": "Q8IYU2-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SDVDVEDAMGQTALHVACQN", "down_seq": "HKTTVQCLLDSGADINRPNV", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "S", "comment": "Impairs ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8IYU2-1.173.173", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IYU2-1.174.174", "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": "Q8IYU2-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LDSGADINRPNVSGATPLYF", "down_seq": "CSHGQRDTAQILLLRGAKYL", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "T", "comment": "Impairs ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "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": "Q8IYU2-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "", "down_seq": "VELPEDNETAVYTLMPMVMA", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "E", "comment": "Monomeric; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IYU2-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IYU2-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IYU2-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IYU2-1.15.15", "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": "Q8IYU2-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IYU2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NYDAQMKSLLRIVRMFCHVF", "down_seq": "IGPSSPSNGIDMGYNGNKTP", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Promotes ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "snv": [ { "evidence": [ { "id": "Q8IYU2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "5", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "104791583", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R332", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "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": "Q8IYU2-1.353.353", "start_pos": 353, "end_pos": 353, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IGPSSPSNGIDMGYNGNKTP", "down_seq": "SQVFKPLELLWHSLDEWLVL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Promotes ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IYU2-1.357.357", "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": "Q8IYU2-1.694.694", "start_pos": 694, "end_pos": 694, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "PVNYQDVASIDPEYAKNLQW", "down_seq": "LDNDISDLGLELTFSVETDV", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "D", "comment": "Monomeric; loss of E3 ubiquitin ligase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8IYU2-1.689.689", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IYU2-1.704.704", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IYU2-1.706.706", "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": "Q8IYU2-1.704.704", "start_pos": 704, "end_pos": 704, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "DPEYAKNLQWILDNDISDLG", "down_seq": "ELTFSVETDVFGAMEEVPLK", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Dimeric; loss of E3 ubiquitin ligase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IYU2-1.689.689", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IYU2-1.694.694", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IYU2-1.706.706", "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": "Q8IYU2-1.706.706", "start_pos": 706, "end_pos": 706, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "EYAKNLQWILDNDISDLGLE", "down_seq": "TFSVETDVFGAMEEVPLKPG", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Monomeric; loss of E3 ubiquitin ligase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IYU2-1.689.689", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IYU2-1.694.694", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IYU2-1.704.704", "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": "Q8IYU2-1.876.876", "start_pos": 876, "end_pos": 876, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The ubiquitin ligase HACE1 regulates Golgi membrane dynamics during the cell cycle.", "journal": "Nature communications", "date": "2011", "authors": "Tang D, Xiang Y, De Renzis S, Rink J, Zheng G, Zerial M, Wang Y", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "21988917", "url": "https://glygen.org/publication/PubMed/21988917" } ] }, { "title": "Differential expression of a novel ankyrin containing E3 ubiquitin-protein ligase, Hace1, in sporadic Wilms' tumor versus normal kidney.", "journal": "Human molecular genetics", "date": "2004", "authors": "Anglesio MS, Evdokimova V, Melnyk N, Zhang L, Fernandez CV, Grundy PE, Leach S, Marra MA, Brooks-Wilson AR, Penninger J, Sorensen PH", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "15254018", "url": "https://glygen.org/publication/PubMed/15254018" } ] }, { "title": "The E3 ubiquitin-ligase HACE1 catalyzes the ubiquitylation of active Rac1.", "journal": "Developmental cell", "date": "2011", "authors": "Torrino S, Visvikis O, Doye A, Boyer L, Stefani C, Munro P, Bertoglio J, Gacon G, Mettouchi A, Lemichez E", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "Reactome", "id": "R-HSA-9958825", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9958825" } ], "reference": [ { "type": "PubMed", "id": "22036506", "url": "https://glygen.org/publication/PubMed/22036506" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21988917", "url": "https://glygen.org/publication/PubMed/21988917", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15254018", "url": "https://glygen.org/publication/PubMed/15254018", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22036506", "url": "https://glygen.org/publication/PubMed/22036506", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "QNFTIAAVPYTPNLLPTSST", "down_seq": "INMLKLPEYPSKEILKDRLL", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Loss of E3 ubiquitin ligase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "21988917", "url": "https://glygen.org/publication/PubMed/21988917" }, { "database": "PubMed", "id": "15254018", "url": "https://glygen.org/publication/PubMed/15254018" }, { "database": "PubMed", "id": "22036506", "url": "https://glygen.org/publication/PubMed/22036506" } ] }, { "sequence_org": "C", "sequence_mut": "S", "comment": "Loss of E3 ubiquitin ligase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "21988917", "url": "https://glygen.org/publication/PubMed/21988917" }, { "database": "PubMed", "id": "15254018", "url": "https://glygen.org/publication/PubMed/15254018" }, { "database": "PubMed", "id": "22036506", "url": "https://glygen.org/publication/PubMed/22036506" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IYU2-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.", "journal": "Nature structural & molecular biology", "date": "2024-02", "authors": "D\u00fcring Jonas, Wolter Madita, Toplak Julia J, Torres Camilo, Dybkov Olexandr, Fokkens Thornton J, Bohnsack Katherine E, Urlaub Henning, Steinchen Wieland, Dienemann Christian, Lorenz Sonja", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MERAMEQ", "down_seq": "NRLTRSLRRARTVELPEDNE", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "Exists as a mixture of monomer and dimer; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] }, { "sequence_org": "L", "sequence_mut": "D", "comment": "Exists as a mixture of monomer and dimer; promotes autoubiquitination and ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "38332367", "url": "https://glygen.org/publication/PubMed/38332367" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8IYU2-1.11.11", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IYU2-1.14.14", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IYU2-1.15.15", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IYU2-1.20.20", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IYU2-1.906.906", "start_pos": 906, "end_pos": 906, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PSKEILKDRLLVALHCGSYG", "down_seq": "TMA", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Abolishes ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8IYU2-1.907.909", "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": "Q8IYU2-1.907.909", "start_pos": 907, "end_pos": 909, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "date": "2023-09", "authors": "Singh Sunil, Machida Satoru, Tulsian Nikhil Kumar, Choong Yeu Khai, Ng Joel, Shankar Srihari, Liu Yaochen, Chandiramani Krisha Vashdev, Shi Jian, Sivaraman J", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "RefSeq", "id": "NP_001308009", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308009" } ], "reference": [ { "type": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "TMA", "start_aa": "T", "up_seq": "SKEILKDRLLVALHCGSYGY", "down_seq": "", "mutagenesis": [ { "sequence_org": "TMA", "sequence_mut": "", "comment": "Abolishes ubiquitination of RAC1.", "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" }, { "database": "PubMed", "id": "37537642", "url": "https://glygen.org/publication/PubMed/37537642" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8IYU2-1.906.906", "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": "Q8IYU2-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IYU2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "SPSNGIDMGYNGNKTPRSQV", "down_seq": "KPLELLWHSLDEWLVLIATE", "snv": [ { "evidence": [ { "id": "Q8IYU2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "104791509", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "F357", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IYU2-1.353.353", "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": "Q8IYU2-1.642.642", "start_pos": 642, "end_pos": 642, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IYU2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GTTFQPNSNSYVNPDHLNYF", "down_seq": "FAGQILGLALNHRQLVNIYF", "snv": [ { "evidence": [ { "id": "Q8IYU2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2" } ], "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": "6", "chr_pos": "104772015", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R642", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IYU2-1.689.689", "start_pos": 689, "end_pos": 689, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IYU2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HILGIPVNYQDVASIDPEYA", "down_seq": "NLQWILDNDISDLGLELTFS", "snv": [ { "evidence": [ { "id": "Q8IYU2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IYU2" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "K", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "6", "chr_pos": "104771339", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K689", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8IYU2-1.694.694", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IYU2-1.704.704", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IYU2-1.706.706", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IYU2-1.385.385", "start_pos": 385, "end_pos": 385, "uniprot_canonical_ac": "Q8IYU2-1", "length": 909, "uniprot_id": "HACE1_HUMAN", "protein_name": "E3 ubiquitin-protein ligase HACE1", "refseq_ac": "NP_001308009", "refseq_name": "E3 ubiquitin-protein ligase HACE1 isoform b", "gene_name": "HACE1", "gene_names_uniprotkb": "HACE1; KIAA1320", "gene_names_refseq": "HACE1; SPPRS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IYU2", "url": "https://www.uniprot.org/uniprotkb/Q8IYU2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Group-I PAKs-mediated phosphorylation of HACE1 at serine 385 regulates its oligomerization state and Rac1 ubiquitination.", "journal": "Scientific reports", "date": "2018", "authors": "Acosta MI, Urbach S, Doye A, Ng YW, Boudeau J, Mettouchi A, Debant A, Manser E, Visvikis O, Lemichez E", "evidence": [ { "database": "iPTMnet", "id": "Q8IYU2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYU2" } ], "reference": [ { "type": "PubMed", "id": "29362425", "url": "https://glygen.org/publication/PubMed/29362425" } ] } ], "crossref": [ { "id": "Q8IYU2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYU2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "29362425", "url": "https://glygen.org/publication/PubMed/29362425", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HSLDEWLVLIATELMKNKRD", "down_seq": "TEITSILLKQKGQDQDAASI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13153-1", "kinase_gene_name": "PAK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8IYU2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IYU2" }, { "database": "PubMed", "id": "29362425", "url": "https://glygen.org/publication/PubMed/29362425" } ], "site_lbl": "Ser385" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "907", "end_pos": "909" } ] }, { "type": "snv", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "689", "end_pos": "689" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "385", "end_pos": "385" } ] } ], "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": "Q68CP4-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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": "NLTVYWKSECCYHCLFQVLV", "down_seq": "VPQSPKAGKPSAAAASVSTQ", "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": "Asn114", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q68CP4-1.94.94", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q68CP4-1.107.107", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 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": "Q68CP4-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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": "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": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4#ptm_processing" }, { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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" } ] } ], "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": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "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": "8VKJ", "url": "https://www.rcsb.org/structure/8VKJ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLG", "url": "https://www.rcsb.org/structure/8VLG", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLI", "url": "https://www.rcsb.org/structure/8VLI", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLU", "url": "https://www.rcsb.org/structure/8VLU", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLY", "url": "https://www.rcsb.org/structure/8VLY", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLV", "url": "https://www.rcsb.org/structure/8VLV", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8TU9", "url": "https://www.rcsb.org/structure/8TU9", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VKJ|B|142", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLG|B|142", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLI|B|142", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLU|A|142", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLU|B|142", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLY|B|142", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLV|B|142", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8TU9|B|114", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8TU9|A|114", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GKPSAAAASVSTQHGSILQL", "down_seq": "DTLEEKEVCRLEYRFGEFGN", "glycosylation": [ { "glytoucan_ac": "G92050GC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AGKPSAAAASVSTQHGSILQLNDTLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn142", "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": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=8VKJ&bu=0&command=select+.B:142;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn142", "evidence": [ { "id": "Q68CP4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q68CP4#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": "8VKJ", "database": "PDB", "url": "https://www.rcsb.org/structure/8VKJ" }, { "id": "8VLG", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLG" }, { "id": "8VLI", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLI" }, { "id": "8VLU", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLU" }, { "id": "8VLY", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLY" }, { "id": "8VLV", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLV" }, { "id": "8TU9", "database": "PDB", "url": "https://www.rcsb.org/structure/8TU9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q68CP4-1.151.151", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q68CP4-1.162.162", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 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", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CP4-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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": "1307", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ], "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": "1307", "url": "https://glyconnect.expasy.org/browser/proteins/1307", "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": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "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": "8VKJ", "url": "https://www.rcsb.org/structure/8VKJ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLG", "url": "https://www.rcsb.org/structure/8VLG", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLI", "url": "https://www.rcsb.org/structure/8VLI", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLU", "url": "https://www.rcsb.org/structure/8VLU", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLY", "url": "https://www.rcsb.org/structure/8VLY", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLV", "url": "https://www.rcsb.org/structure/8VLV", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8TU9", "url": "https://www.rcsb.org/structure/8TU9", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VKJ|B|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VKJ|A|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLG|B|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLG|A|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLI|B|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLI|A|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLU|A|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLU|B|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLY|B|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLY|A|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLV|B|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLV|A|162", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8TU9|B|134", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8TU9|A|134", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NDTLEEKEVCRLEYRFGEFG", "down_seq": "YSLLVKNIHNGVSEIACDLA", "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": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "Asn162", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1307", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "Asn162", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1307", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "Asn162", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1307", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "FGEFGnYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "evidence": [ { "id": "37074911", "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": "Asn162", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1307", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FGEFGNYSLLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "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": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=8VKJ&bu=0&command=select+.B:162;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn162", "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": "Q68CP4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q68CP4#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": "8VKJ", "database": "PDB", "url": "https://www.rcsb.org/structure/8VKJ" }, { "id": "8VLG", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLG" }, { "id": "8VLI", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLI" }, { "id": "8VLU", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLU" }, { "id": "8VLY", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLY" }, { "id": "8VLV", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLV" }, { "id": "8TU9", "database": "PDB", "url": "https://www.rcsb.org/structure/8TU9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q68CP4-1.142.142", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q68CP4-1.151.151", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q68CP4-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68CP4-1.179.179", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 16 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 15 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 15 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 15 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 15 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 15 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CP4-1.461.461", "start_pos": 461, "end_pos": 461, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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": "1307", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ], "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": "1307", "url": "https://glyconnect.expasy.org/browser/proteins/1307", "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": "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": "8VLU", "url": "https://www.rcsb.org/structure/8VLU", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLV", "url": "https://www.rcsb.org/structure/8VLV", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8TU9", "url": "https://www.rcsb.org/structure/8TU9", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLU|B|461", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLV|B|461", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLV|A|461", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8TU9|B|433", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8TU9|A|433", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PGCPTGYLGPGGIGDFGKYP", "down_seq": "CTGGAAGYIDRLLLGDDHLY", "glycosylation": [ { "glytoucan_ac": "G27947YN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YPnCTGGAAGYIDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn461", "evidence": [ { "id": "37074911", "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": "YPnCTGGAAGYIDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn461", "evidence": [ { "id": "37074911", "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": "YPnCTGGAAGYIDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn461", "evidence": [ { "id": "37074911", "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": "Asn461", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1307", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ] }, { "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": "Asn461", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1307", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1307" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YPnCTGGAAGYIDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn461", "evidence": [ { "id": "37074911", "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": "YPNCTGGAAGYIDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn461", "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": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=8VLU&bu=0&command=select+.B:461;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn461", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "8VLU", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLU" }, { "id": "8VLV", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLV" }, { "id": "8TU9", "database": "PDB", "url": "https://www.rcsb.org/structure/8TU9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q68CP4-1.462.462", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q68CP4-1.474.474", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q68CP4-1.479.479", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 8 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 7 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 7 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 7 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 7 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CP4-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8JKV", "url": "https://www.rcsb.org/structure/8JKV", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8JL1", "url": "https://www.rcsb.org/structure/8JL1", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8JL3", "url": "https://www.rcsb.org/structure/8JL3", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8JL4", "url": "https://www.rcsb.org/structure/8JL4", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VKJ", "url": "https://www.rcsb.org/structure/8VKJ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLG", "url": "https://www.rcsb.org/structure/8VLG", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLI", "url": "https://www.rcsb.org/structure/8VLI", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLU", "url": "https://www.rcsb.org/structure/8VLU", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLY", "url": "https://www.rcsb.org/structure/8VLY", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8W4A", "url": "https://www.rcsb.org/structure/8W4A", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VLV", "url": "https://www.rcsb.org/structure/8VLV", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8JKV|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8JKV|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8JL1|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8JL1|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8JL3|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8JL3|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8JL4|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8JL4|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VKJ|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VKJ|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLG|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLI|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLI|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLU|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLU|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLY|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLY|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8W4A|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8W4A|A|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLV|B|94", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VLV|A|94", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HAELKMDQALLLIHNELLWT", "down_seq": "LTVYWKSECCYHCLFQVLVN", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=8JKV&bu=0&command=select+.B:94;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn94", "evidence": [ { "id": "Q68CP4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q68CP4#ptm_processing" }, { "id": "8JKV", "database": "PDB", "url": "https://www.rcsb.org/structure/8JKV" }, { "id": "8JL1", "database": "PDB", "url": "https://www.rcsb.org/structure/8JL1" }, { "id": "8JL3", "database": "PDB", "url": "https://www.rcsb.org/structure/8JL3" }, { "id": "8JL4", "database": "PDB", "url": "https://www.rcsb.org/structure/8JL4" }, { "id": "8VKJ", "database": "PDB", "url": "https://www.rcsb.org/structure/8VKJ" }, { "id": "8VLG", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLG" }, { "id": "8VLI", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLI" }, { "id": "8VLU", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLU" }, { "id": "8VLY", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLY" }, { "id": "8W4A", "database": "PDB", "url": "https://www.rcsb.org/structure/8W4A" }, { "id": "8VLV", "database": "PDB", "url": "https://www.rcsb.org/structure/8VLV" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q68CP4-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q68CP4-1.114.114", "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", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CP4-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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": "Q68CP4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CP4" } ], "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": "Q68CP4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CP4", "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": "Q68CP4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CP4" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "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": "Q68CP4-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "HNELLWTNLTVYWKSECCYH", "down_seq": "LFQVLVNVPQSPKAGKPSAA", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "Loss of intralysosomal proteolytic cleavage and enzymatic activity. Reduced oligomer formation.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q68CP4-1.94.94", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q68CP4-1.114.114", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CP4-1.151.151", "start_pos": 151, "end_pos": 151, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "VSTQHGSILQLNDTLEEKEV", "down_seq": "RLEYRFGEFGNYSLLVKNIH", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "Loss of intralysosomal proteolytic cleavage and enzymatic activity. Reduced oligomer formation.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q68CP4-1.142.142", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CP4-1.162.162", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CP4-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "EFGNYSLLVKNIHNGVSEIA", "down_seq": "DLAVNEDPVDSNLPVSIAFL", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "Loss of intralysosomal proteolytic cleavage and enzymatic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q68CP4-1.162.162", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68CP4-1.177.177", "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": "Q68CP4-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SLDDFNNWISKAISSRETDR", "down_seq": "INSELGSPSRTDPLDGDVQP", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "Displayed both lysosomal and plasma membrane localization, reduced intralysosomal proteolytic cleavage and enzymatic activity; when associated with A-209.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q68CP4-1.237.237", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q68CP4-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CP4-1.245.245", "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": "Q68CP4-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LDDFNNWISKAISSRETDRL", "down_seq": "NSELGSPSRTDPLDGDVQPA", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "A", "comment": "Displayed both lysosomal and plasma membrane localization, reduced intralysosomal proteolytic cleavage and enzymatic activity; when associated with A-208.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q68CP4-1.236.236", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q68CP4-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q68CP4-1.245.245", "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": "Q68CP4-1.297.297", "start_pos": 297, "end_pos": 297, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IALILMVFVNYGGGKYWYFK", "down_seq": "ASWNGLTVADLVFPWFVFIM", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Loss of enzymatic activity, but correctly targeted and processed.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q68CP4-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CP4-1.302.302", "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": "Q68CP4-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "FVFIMGSSIFLSMTSILQRG", "down_seq": "SKFRLLGKIAWRSFLLICIG", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "No loss of intralysosomal proteolytic cleavage and enzymatic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q68CP4-1.338.338", "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": "Q68CP4-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "VTYFVVAVLELLFAKPVPEH", "down_seq": "ASERSCLSLRDITSSWPQWL", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "No loss of intralysosomal proteolytic cleavage and enzymatic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q68CP4-1.409.409", "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": "Q68CP4-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "GCPTGYLGPGGIGDFGKYPN", "down_seq": "TGGAAGYIDRLLLGDDHLYQ", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "Complete loss of intralysosomal proteolytic cleavage and enzymatic activity. Reduced oligomer formation.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q68CP4-1.461.461", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q68CP4-1.474.474", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68CP4-1.479.479", "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": "Q68CP4-1.479.479", "start_pos": 479, "end_pos": 479, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "YPNCTGGAAGYIDRLLLGDD", "down_seq": "LYQHPSSAVLYHTEVAYDPE", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Loss of intralysosomal proteolytic cleavage and enzymatic activity, retained in the endoplasmic reticulum.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68CP4-1.461.461", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q68CP4-1.462.462", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q68CP4-1.474.474", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68CP4-1.496.496", "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": "Q68CP4-1.633.633", "start_pos": 633, "end_pos": 633, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "Reactome", "id": "R-HSA-2024096", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2024096" } ], "reference": [ { "type": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GHEVFENYFPFQWKLKDNQS", "down_seq": "KEHLTQNIVATALWVLIAYI", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Loss of intralysosomal proteolytic cleavage and enzymatic activity, retained in the endoplasmic reticulum.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "20650889", "url": "https://glygen.org/publication/PubMed/20650889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q68CP4-1.652.663", "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": "Q68CP4-1.652.663", "start_pos": 652, "end_pos": 663, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "YILYRKKIFWKI", "start_aa": "Y", "up_seq": "SHKEHLTQNIVATALWVLIA", "down_seq": "", "mutagenesis": [ { "sequence_org": "YILYRKKIFWKI", "sequence_mut": "", "comment": "Loss of intralysosomal proteolytic cleavage and enzymatic activity. Localized in the plasma membrane.", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q68CP4-1.633.633", "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": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CP4-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FGEFGNYSLLVKNIHNGVSE", "down_seq": "ACDLAVNEDPVDSNLPVSIA", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43161474", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I177", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q68CP4-1.162.162", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68CP4-1.179.179", "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": "Q68CP4-1.299.299", "start_pos": 299, "end_pos": 299, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LILMVFVNYGGGKYWYFKHA", "down_seq": "WNGLTVADLVFPWFVFIMGS", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43178118", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S299", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q68CP4-1.297.297", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q68CP4-1.302.302", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CP4-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs376476836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376476836", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376476836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376476836", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376476836", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376476836#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376476836", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376476836", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs376476836", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs376476836", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MVFVNYGGGKYWYFKHASWN", "down_seq": "LTVADLVFPWFVFIMGSSIF", "snv": [ { "evidence": [ { "id": "rs376476836", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376476836" }, { "id": "rs376476836", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376476836" }, { "id": "rs376476836", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376476836#frequency_tab" }, { "id": "rs376476836", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376476836" }, { "id": "rs376476836", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs376476836" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "8", "chr_pos": "43199414", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G302", "disease": [ { "disease_id": "DOID:0111393", "recommended_name": { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "mucopolysaccharidosis type IIIC", "description": "A mucopolysaccharidosis III that has_material_basis_in homozygous or compound heterozygous mutation in the HGSNAT gene on chromosome 8p11.2-p11.1." }, "synonyms": [ { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "HGSNAT deficiency", "description": "" }, { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "MPS3C", "description": "" }, { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "MPSIIIC", "description": "" }, { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "Mucopolysaccharidosis type 3C", "description": "" }, { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "Sanfilippo syndrome type C", "description": "" }, { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "mucopolysaccharidosis type IIIC (Sanfilippo C)", "description": "" }, { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "Acetyl-CoA alpha-glucosaminide acetyltransferase deficiency", "description": "" }, { "id": "DOID:0111393", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111393", "name": "Heparan-alpha-glucosaminide N-acetyltransferase deficiency", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "mucopolysaccharidosis type 3C", "description": "A rare autosomal recessive lysosomal storage disease caused by deficiency of the enzyme acetyl-CoA:alpha-glucosaminide acetyltransferase. It is characterized by behavioral changes, sleep disturbances, and mental developmental delays." }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "HGSNAT deficiency", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "MPS III C", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "MPS3C", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "MPSIIIC", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "Sanfilippo C", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "Sanfilippo syndrome type C", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "heparan-alpha-glucosaminide N-acetyltransferase deficiency", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "mucopolysaccharidosis type 3C", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "mucopolysaccharidosis type IIIC", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "Acetyl-CoA alpha-glucosaminide n-acetyltransferase deficiency", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "MPS IIIC", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "Mucopoly-saccharidosis type 3C", "description": "" }, { "id": "MONDO:0009657", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657", "name": "mucopolysaccharidosis, type IIIC", "description": "" }, { "id": "MIM:252930", "resource": "MIM", "url": "https://www.omim.org/entry/252930", "name": "Mucopolysaccharidosis 3C", "description": "Mucopolysaccharidosis 3C" } ], "unlinked_id_list": [], "evidence": [ { "id": "0009657", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009657" }, { "id": "252930", "database": "MIM", "url": "https://www.omim.org/entry/252930" }, { "id": "138050", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/138050#disease" }, { "id": "0111393", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111393" } ] }, { "disease_id": "DOID:0110389", "recommended_name": { "id": "DOID:0110389", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110389", "name": "retinitis pigmentosa 73", "description": "A retinitis pigmentosa that has_material_basis_in mutation in the HGSNAT gene on chromosome 8p11." }, "synonyms": [ { "id": "DOID:0110389", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110389", "name": "RP73", "description": "" }, { "id": "MONDO:0014687", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014687", "name": "retinitis pigmentosa 73", "description": "Any retinitis pigmentosa in which the cause of the disease is a mutation in the HGSNAT gene." }, { "id": "MONDO:0014687", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014687", "name": "HGSNAT retinitis pigmentosa", "description": "" }, { "id": "MONDO:0014687", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014687", "name": "RP73", "description": "" }, { "id": "MONDO:0014687", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014687", "name": "retinitis pigmentosa 73", "description": "" }, { "id": "MONDO:0014687", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014687", "name": "retinitis pigmentosa caused by mutation in HGSNAT", "description": "" }, { "id": "MONDO:0014687", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014687", "name": "retinitis pigmentosa type 73", "description": "" }, { "id": "MIM:616544", "resource": "MIM", "url": "https://www.omim.org/entry/616544", "name": "Retinitis pigmentosa 73", "description": "Retinitis pigmentosa 73" } ], "unlinked_id_list": [], "evidence": [ { "id": "616544", "database": "MIM", "url": "https://www.omim.org/entry/616544" }, { "id": "0110389", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0110389" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q68CP4-1.297.297", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q68CP4-1.299.299", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "Q68CP4-1.338.338", "start_pos": 338, "end_pos": 338, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GSSIFLSMTSILQRGCSKFR", "down_seq": "LGKIAWRSFLLICIGIIIVN", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43182145", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L338", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q68CP4-1.333.333", "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": "Q68CP4-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GRSGQARAAERAAGMSGAGR", "down_seq": "LAALLLAASVLSAALLAPGG", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43140600", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A35", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CP4-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VLELLFAKPVPEHCASERSC", "down_seq": "SLRDITSSWPQWLLILVLEG", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43191571", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L409", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q68CP4-1.402.402", "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": "Q68CP4-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GDFGKYPNCTGGAAGYIDRL", "down_seq": "LGDDHLYQHPSSAVLYHTEV", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43193799", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L474", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q68CP4-1.461.461", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q68CP4-1.462.462", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CP4-1.479.479", "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": "Q68CP4-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GDDHLYQHPSSAVLYHTEVA", "down_seq": "DPEGILGTINSIVMAFLGVQ", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43196970", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y496", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q68CP4-1.479.479", "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": "Q68CP4-1.584.584", "start_pos": 584, "end_pos": 584, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "NLWSLSYVTTLSSFAFFILL", "down_seq": "LYPVVDVKGLWTGTPFFYPG", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43199411", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V584", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CP4-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CP4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "APGGSSGRDAQAAPPRDLDK", "down_seq": "RHAELKMDQALLLIHNELLW", "snv": [ { "evidence": [ { "id": "Q68CP4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CP4" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, gag-related).", "chr_id": "8", "chr_pos": "43147043", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K72", "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": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CP4-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "iPTMnet", "id": "Q68CP4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CP4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CP4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CP4", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WISKAISSRETDRLINSELG", "down_seq": "PSRTDPLDGDVQPATWRLSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q68CP4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CP4" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q68CP4-1.236.236", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q68CP4-1.237.237", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68CP4-1.245.245", "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": "Q68CP4-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "Q68CP4-1", "length": 663, "uniprot_id": "HGNAT_HUMAN", "protein_name": "Heparan-alpha-glucosaminide N-acetyltransferase", "refseq_ac": "NP_689632", "refseq_name": "heparan-alpha-glucosaminide N-acetyltransferase isoform 1 precursor", "gene_name": "HGSNAT", "gene_names_uniprotkb": "HGSNAT; TMEM76", "gene_names_refseq": "HGNAT; HGSNAT; MPS3C; RP73; TMEM76", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" } ], "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": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "iPTMnet", "id": "Q68CP4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CP4" } ], "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": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "database": "iPTMnet", "id": "Q68CP4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CP4" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CP4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CP4", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKAISSRETDRLINSELGSP", "down_seq": "RTDPLDGDVQPATWRLSALP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CP4", "url": "https://www.uniprot.org/uniprotkb/Q68CP4" }, { "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": "Q68CP4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CP4" } ], "site_lbl": "Ser245" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "652", "end_pos": "663" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q68CP4-1.236.236", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q68CP4-1.237.237", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68CP4-1.243.243", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2PYH4-1.1105.1105", "start_pos": 1105, "end_pos": 1105, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "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": "A2PYH4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2PYH4" } ], "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": "A2PYH4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2PYH4" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "A2PYH4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2PYH4" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2PYH4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2PYH4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201592712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201592712", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201592712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201592712", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201592712", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201592712#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201592712", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201592712", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DIQQKLTVFYLEPKRFGNQI", "down_seq": "MQRKSETQISHSKHSDISTI", "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": "Thr1105", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "A2PYH4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2PYH4" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" } ] } ], "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "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": "1", "chr_pos": "91313427", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T1105", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs201592712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201592712" }, { "id": "rs201592712", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201592712" }, { "id": "rs201592712", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201592712#frequency_tab" }, { "id": "rs201592712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201592712" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "1", "chr_pos": "91313427", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1105", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2PYH4-1.1002.1002", "start_pos": 1002, "end_pos": 1002, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VMYLPKYELKVEQITRYSDT", "down_seq": "AEILVTVILRNFEQLQTKRT", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "91315950", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1002", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "A2PYH4-1.999.999", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1034.1034", "start_pos": 1034, "end_pos": 1034, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "FEQLQTKRTASDSHYVTLII", "down_seq": "DADNQVVYLHKITDSVLLKA", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "91315855", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1034", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "A2PYH4-1.1045.1045", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "A2PYH4-1.1047.1047", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1045.1045", "start_pos": 1045, "end_pos": 1045, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201222637", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201222637", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201222637", "url": "https://www.ensembl.org/id/rs201222637", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "DSHYVTLIIGDADNQVVYLH", "down_seq": "ITDSVLLKAGSWAKKIAVKR", "snv": [ { "evidence": [ { "id": "rs201222637", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201222637" }, { "id": "rs201222637", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs201222637" } ], "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": "1", "chr_pos": "91315820", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1045", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "A2PYH4-1.1034.1034", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "A2PYH4-1.1047.1047", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1047.1047", "start_pos": 1047, "end_pos": 1047, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HYVTLIIGDADNQVVYLHKI", "down_seq": "DSVLLKAGSWAKKIAVKRAL", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "1", "chr_pos": "91315815", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1047", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "A2PYH4-1.1034.1034", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "A2PYH4-1.1045.1045", "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": "A2PYH4-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1321370124", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1321370124", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1321370124", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1321370124#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1321370124", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1321370124", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AFPSDKYEQDDLNLEGVGNN", "down_seq": "LSHIAGKLTYASQKYKNHIG", "snv": [ { "evidence": [ { "id": "rs1321370124", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1321370124" }, { "id": "rs1321370124", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1321370124#frequency_tab" }, { "id": "rs1321370124", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1321370124" } ], "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": "1", "chr_pos": "91394250", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D113", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "A2PYH4-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "A2PYH4-1.132.132", "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": "A2PYH4-1.1145.1145", "start_pos": 1145, "end_pos": 1145, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IAGPNKGTTASKKPGNRECN", "down_seq": "LCKSKHTCGHDCCKIGVAQK", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HLC->NLC).", "chr_id": "1", "chr_pos": "91277021", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H1145", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "A2PYH4-1.1150.1150", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "A2PYH4-1.1155.1155", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1150.1150", "start_pos": 1150, "end_pos": 1150, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1666887436", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1666887436", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1666887436", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1666887436#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KGTTASKKPGNRECNHLCKS", "down_seq": "HTCGHDCCKIGVAQKSEIKE", "snv": [ { "evidence": [ { "id": "rs1666887436", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1666887436" }, { "id": "rs1666887436", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1666887436#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KHT->NHT).", "chr_id": "1", "chr_pos": "91277004", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1150", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "A2PYH4-1.1145.1145", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "A2PYH4-1.1155.1155", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1155.1155", "start_pos": 1155, "end_pos": 1155, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767743030", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767743030", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767743030", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767743030", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767743030", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767743030", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SKKPGNRECNHLCKSKHTCG", "down_seq": "DCCKIGVAQKSEIKESTISS", "snv": [ { "evidence": [ { "id": "rs767743030", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767743030" }, { "id": "rs767743030", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767743030" }, { "id": "rs767743030", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767743030" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HDC->NDC).", "chr_id": "1", "chr_pos": "91276991", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1155", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "A2PYH4-1.1145.1145", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "A2PYH4-1.1150.1150", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1176.1176", "start_pos": 1176, "end_pos": 1176, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs892233117", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs892233117", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs892233117", "url": "https://www.ncbi.nlm.nih.gov/snp/rs892233117#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DCCKIGVAQKSEIKESTISS", "down_seq": "LSDLRNRNAVSSVPPVKRLK", "snv": [ { "evidence": [ { "id": "rs892233117", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs892233117" }, { "id": "rs892233117", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs892233117#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YLS->NLS).", "chr_id": "1", "chr_pos": "91276690", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1176", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "A2PYH4-1.1184.1184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1184.1184", "start_pos": 1184, "end_pos": 1184, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1056200813", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1056200813", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1056200813", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1056200813#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QKSEIKESTISSYLSDLRNR", "down_seq": "AVSSVPPVKRLKIQMNKSQS", "snv": [ { "evidence": [ { "id": "rs1056200813", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1056200813" }, { "id": "rs1056200813", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1056200813#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRN->NRS).", "chr_id": "1", "chr_pos": "91276665", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "A2PYH4-1.1176.1176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1220.1220", "start_pos": 1220, "end_pos": 1220, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1570740284", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1570740284", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1570740284", "url": "https://www.ensembl.org/id/rs1570740284", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NKSQSVDLKEFGFTPKPSLP", "down_seq": "ISRSEYLNISELPIMEQWDQ", "snv": [ { "evidence": [ { "id": "rs1570740284", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1570740284" }, { "id": "rs1570740284", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1570740284" } ], "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": "1", "chr_pos": "91274739", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1220", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DLNLEGVGNNDLSHIAGKLT", "down_seq": "ASQKYKNHIGTEIAPEKSVP", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (YAS->NAS).", "chr_id": "1", "chr_pos": "91394220", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y123", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "A2PYH4-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "A2PYH4-1.132.132", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1263.1263", "start_pos": 1263, "end_pos": 1263, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2523694503", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2523694503", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IYGKVRQEPSEYQDKEVLNV", "down_seq": "FELGNEVWDDFDDENLEVTS", "snv": [ { "evidence": [ { "id": "rs2523694503", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2523694503" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVN->NVT).", "chr_id": "1", "chr_pos": "91267840", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1263", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1292.1292", "start_pos": 1292, "end_pos": 1292, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "DDFDDENLEVTSFSTDTEKT", "down_seq": "ISGFGNTLSSSTRGSKLPLQ", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KIS->NIS).", "chr_id": "1", "chr_pos": "91267752", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K1292", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "A2PYH4-1.1301.1301", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1301.1301", "start_pos": 1301, "end_pos": 1301, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1419171546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419171546", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1419171546", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1419171546", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VTSFSTDTEKTKISGFGNTL", "down_seq": "SSTRGSKLPLQESKSKFQRE", "snv": [ { "evidence": [ { "id": "rs1419171546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419171546" }, { "id": "rs1419171546", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1419171546" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "1", "chr_pos": "91266089", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "A2PYH4-1.1292.1292", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1663351797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1663351797", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1663351797", "url": "https://www.ensembl.org/id/rs1663351797", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "NDLSHIAGKLTYASQKYKNH", "down_seq": "GTEIAPEKSVPDDTKLVNFA", "snv": [ { "evidence": [ { "id": "rs1663351797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1663351797" }, { "id": "rs1663351797", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1663351797" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHI->NHT).", "chr_id": "1", "chr_pos": "91394192", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I132", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "A2PYH4-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "A2PYH4-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "A2PYH4-1.152.152", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1334.1334", "start_pos": 1334, "end_pos": 1334, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1570698496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1570698496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1570698496", "url": "https://www.ensembl.org/id/rs1570698496", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SKSKFQREMSNSFVSSHEMS", "down_seq": "ISLSNSAMPKFSASSMTKLP", "snv": [ { "evidence": [ { "id": "rs1570698496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1570698496" }, { "id": "rs1570698496", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1570698496" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DIS->NIS).", "chr_id": "1", "chr_pos": "91262567", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1334", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1404.1404", "start_pos": 1404, "end_pos": 1404, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768147001", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768147001", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768147001", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768147001", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768147001", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768147001", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FSEKNPNSSNYKKVDFFIRN", "down_seq": "ECKKEVDFSMYHPDDEADEM", "snv": [ { "evidence": [ { "id": "rs768147001", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768147001" }, { "id": "rs768147001", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768147001" }, { "id": "rs768147001", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768147001" } ], "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 (SEC->NEC).", "chr_id": "1", "chr_pos": "91262268", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1404", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "A2PYH4-1.1424.1424", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.1424.1424", "start_pos": 1424, "end_pos": 1424, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "SECKKEVDFSMYHPDDEADE", "down_seq": "KSLLGIFDGIF", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "1", "chr_pos": "91261326", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M1424", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "A2PYH4-1.1404.1404", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "A2PYH4-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1181511413", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1181511413", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1181511413", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1181511413", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "IGTEIAPEKSVPDDTKLVNF", "down_seq": "EDKGESTSVFRKRLFKISDN", "snv": [ { "evidence": [ { "id": "rs1181511413", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1181511413" }, { "id": "rs1181511413", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1181511413" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFA->NFS).", "chr_id": "1", "chr_pos": "91394133", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A152", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "A2PYH4-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "A2PYH4-1.163.163", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PDDTKLVNFAEDKGESTSVF", "down_seq": "KRLFKISDNIHGSAYSNDNE", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "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": "1", "chr_pos": "91394099", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R163", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "A2PYH4-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "A2PYH4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "A2PYH4-1.182.182", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1000525728", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1000525728", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1000525728", "url": "https://www.ensembl.org/id/rs1000525728", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DKGESTSVFRKRLFKISDNI", "down_seq": "GSAYSNDNELDSHIGSVKIV", "snv": [ { "evidence": [ { "id": "rs1000525728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1000525728" }, { "id": "rs1000525728", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1000525728" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HGS->NGS).", "chr_id": "1", "chr_pos": "91385809", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H174", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "A2PYH4-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "A2PYH4-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "A2PYH4-1.184.184", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1489051593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1489051593", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1489051593", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1489051593#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1489051593", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1489051593", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FRKRLFKISDNIHGSAYSND", "down_seq": "ELDSHIGSVKIVQTEMNKGK", "snv": [ { "evidence": [ { "id": "rs1489051593", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1489051593" }, { "id": "rs1489051593", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1489051593#frequency_tab" }, { "id": "rs1489051593", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1489051593" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDN->NDS).", "chr_id": "1", "chr_pos": "91385784", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N182", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "A2PYH4-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "A2PYH4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "A2PYH4-1.184.184", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1662128175", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1662128175", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1662128175", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1662128175", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KRLFKISDNIHGSAYSNDNE", "down_seq": "DSHIGSVKIVQTEMNKGKSR", "snv": [ { "evidence": [ { "id": "rs1662128175", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1662128175" }, { "id": "rs1662128175", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1662128175" } ], "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": "1", "chr_pos": "91385778", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "A2PYH4-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "A2PYH4-1.182.182", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1156242942", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1156242942", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1156242942", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1156242942", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HIGSVKIVQTEMNKGKSRNY", "down_seq": "NSKQKFQYSANVFTANNAFS", "snv": [ { "evidence": [ { "id": "rs1156242942", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1156242942" }, { "id": "rs1156242942", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1156242942" } ], "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 (SNS->NNS).", "chr_id": "1", "chr_pos": "91385709", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S207", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MFKAPSFSVAFQPHDIQEVT", "down_seq": "NGLGSLKAVTEIPAKFRSIF", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "91385226", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E255", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "A2PYH4-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "A2PYH4-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "A2PYH4-1.268.268", "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": "A2PYH4-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs753477544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753477544", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753477544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753477544", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753477544", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753477544", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "APSFSVAFQPHDIQEVTENG", "down_seq": "GSLKAVTEIPAKFRSIFKEF", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "rs753477544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753477544" }, { "id": "rs753477544", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753477544" }, { "id": "rs753477544", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753477544" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGL->NGS).", "chr_id": "1", "chr_pos": "91385216", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L258", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "A2PYH4-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "A2PYH4-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "A2PYH4-1.268.268", "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": "A2PYH4-1.260.260", "start_pos": 260, "end_pos": 260, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SFSVAFQPHDIQEVTENGLG", "down_seq": "LKAVTEIPAKFRSIFKEFPY", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "91385210", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S260", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "A2PYH4-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "A2PYH4-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "A2PYH4-1.268.268", "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": "A2PYH4-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "HDIQEVTENGLGSLKAVTEI", "down_seq": "AKFRSIFKEFPYFNYIQSKA", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "91380982", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P268", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID: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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "A2PYH4-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "A2PYH4-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "A2PYH4-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "A2PYH4-1.284.284", "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": "A2PYH4-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780008884", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780008884", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780008884", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780008884", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780008884", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780008884#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780008884", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780008884", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DCLFSLENLFFEKPDEVENH", "down_seq": "DNEKSLDWFLPPAPLISEIP", "snv": [ { "evidence": [ { "id": "rs780008884", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780008884" }, { "id": "rs780008884", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780008884" }, { "id": "rs780008884", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780008884#frequency_tab" }, { "id": "rs780008884", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780008884" } ], "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": "1", "chr_pos": "91396401", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P26", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1421776011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421776011", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1421776011", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1421776011", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "VTEIPAKFRSIFKEFPYFNY", "down_seq": "QSKAFDDLLYTDRNFVICAP", "snv": [ { "evidence": [ { "id": "rs1421776011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421776011" }, { "id": "rs1421776011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1421776011" } ], "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": "1", "chr_pos": "91380934", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I284", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "A2PYH4-1.268.268", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.391.391", "start_pos": 391, "end_pos": 391, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1187031326", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187031326", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1187031326", "url": "https://www.ensembl.org/id/rs1187031326", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DDLFEIQHAHIIMTTPEKWD", "down_seq": "MTRKWRDNSLVQLVRLFLID", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "rs1187031326", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187031326" }, { "id": "rs1187031326", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1187031326" } ], "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 (SMT->NMT).", "chr_id": "1", "chr_pos": "91378467", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S391", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.421.421", "start_pos": 421, "end_pos": 421, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVQLVRLFLIDEVHIVKDEN", "down_seq": "GPTLEVVVSRMKTVQSVSQT", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "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": "1", "chr_pos": "91378159", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R421", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "A2PYH4-1.422.422", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.422.422", "start_pos": 422, "end_pos": 422, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1661130129", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1661130129", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1661130129", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1661130129#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VQLVRLFLIDEVHIVKDENR", "down_seq": "PTLEVVVSRMKTVQSVSQTL", "snv": [ { "evidence": [ { "id": "rs1661130129", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1661130129" }, { "id": "rs1661130129", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1661130129#frequency_tab" } ], "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": "1", "chr_pos": "91378156", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G422", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "A2PYH4-1.421.421", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.483.483", "start_pos": 483, "end_pos": 483, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765029033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765029033", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765029033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765029033", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765029033", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765029033", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AEDIAEWLSDGERPAVCLKM", "down_seq": "ESHRPVKLQKVVLGFPCSSN", "snv": [ { "evidence": [ { "id": "rs765029033", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765029033" }, { "id": "rs765029033", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765029033" }, { "id": "rs765029033", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765029033" } ], "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": "1", "chr_pos": "91375676", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D483", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.623.623", "start_pos": 623, "end_pos": 623, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs867642174", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867642174", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs867642174", "url": "https://www.ensembl.org/id/rs867642174", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TVGDLPVLFTTSTLAMGVNL", "down_seq": "AHLVVIKSTMHYAGGLFEEY", "snv": [ { "evidence": [ { "id": "rs867642174", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867642174" }, { "id": "rs867642174", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs867642174" } ], "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": "1", "chr_pos": "91352616", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P623", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.644.644", "start_pos": 644, "end_pos": 644, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1657090141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1657090141", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1657090141", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1657090141", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AHLVVIKSTMHYAGGLFEEY", "down_seq": "ETDILQMIGRAGRPQFDTTA", "snv": [ { "evidence": [ { "id": "rs1657090141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1657090141" }, { "id": "rs1657090141", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1657090141" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SET->NET).", "chr_id": "1", "chr_pos": "91352552", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S644", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "A2PYH4-1.661.661", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.661.661", "start_pos": 661, "end_pos": 661, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EEYSETDILQMIGRAGRPQF", "down_seq": "TTATAVIMTRLSTRDKYIQM", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DTT->NTT).", "chr_id": "1", "chr_pos": "91351640", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D661", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "A2PYH4-1.644.644", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.732.732", "start_pos": 732, "end_pos": 732, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1656821734", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1656821734", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1656821734", "url": "https://www.ensembl.org/id/rs1656821734", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1656822133", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1656822133", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1656822133", "url": "https://www.ensembl.org/id/rs1656822133", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VNIAVEWIRSTLLYIRALKN", "down_seq": "SHYGFASGLNKDGIEAKLQE", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "rs1656821734", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1656821734" }, { "id": "rs1656821734", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1656821734" } ], "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": "1", "chr_pos": "91350749", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P732", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "rs1656822133", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1656822133" }, { "id": "rs1656822133", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1656822133" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NSS).", "chr_id": "1", "chr_pos": "91350750", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P732", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=" } ], "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 (NPS->NTS).", "chr_id": "1", "chr_pos": "91350750", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P732", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "A2PYH4-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1219264049", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1219264049", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1219264049", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1219264049", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LESHKLLGQEKRPKMLTSNL", "down_seq": "ITNEDTNYISLTQKFQFAFP", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "rs1219264049", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1219264049" }, { "id": "rs1219264049", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1219264049" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KIT->NIT).", "chr_id": "1", "chr_pos": "91394362", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K75", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.787.787", "start_pos": 787, "end_pos": 787, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IKMDEGVNFKPTEAGRLMAW", "down_seq": "YITFETVKKFYTISGKETLS", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Y", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "1", "chr_pos": "91324743", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y787", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "A2PYH4-1.829.829", "start_pos": 829, "end_pos": 829, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs200685742", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200685742", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200685742", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200685742", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200685742", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200685742", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200685742", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200685742#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200685742", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200685742", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LVTLIAGCKEFLDIQLRINE", "down_seq": "KTLNTLNKDPNRITIRFPME", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" }, { "id": "rs200685742", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200685742" }, { "id": "rs200685742", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200685742" }, { "id": "rs200685742", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200685742" }, { "id": "rs200685742", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200685742#frequency_tab" }, { "id": "rs200685742", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200685742" } ], "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 (KKT->NKT).", "chr_id": "1", "chr_pos": "91323140", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K829", "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": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "A2PYH4-1.835.835", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "A2PYH4-1.841.841", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.835.835", "start_pos": 835, "end_pos": 835, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs994404901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs994404901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs994404901", "url": "https://www.ncbi.nlm.nih.gov/snp/rs994404901#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs994404901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs994404901", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GCKEFLDIQLRINEKKTLNT", "down_seq": "NKDPNRITIRFPMEGRIKTR", "snv": [ { "evidence": [ { "id": "rs994404901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs994404901" }, { "id": "rs994404901", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs994404901#frequency_tab" }, { "id": "rs994404901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs994404901" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTL->NTS).", "chr_id": "1", "chr_pos": "91323123", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L835", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "A2PYH4-1.829.829", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "A2PYH4-1.841.841", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.841.841", "start_pos": 841, "end_pos": 841, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DIQLRINEKKTLNTLNKDPN", "down_seq": "ITIRFPMEGRIKTREMKVNC", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "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": "1", "chr_pos": "91323106", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R841", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "A2PYH4-1.829.829", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "A2PYH4-1.835.835", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.913.913", "start_pos": 913, "end_pos": 913, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761908956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761908956", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761908956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761908956", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761908956", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761908956", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "RWLSDFVAAQEKKFAVLLNS", "down_seq": "ILAKCFRCKLWENSLHVSKQ", "snv": [ { "evidence": [ { "id": "rs761908956", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761908956" }, { "id": "rs761908956", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761908956" }, { "id": "rs761908956", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761908956" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSL->NSS).", "chr_id": "1", "chr_pos": "91319152", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L913", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.949.949", "start_pos": 949, "end_pos": 949, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1651234177", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1651234177", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1651234177", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1651234177#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "HVSKQLEKIGITLSNAIVNA", "down_seq": "LTSFKKIEETDARELELILN", "snv": [ { "evidence": [ { "id": "rs1651234177", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1651234177" }, { "id": "rs1651234177", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1651234177#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAG->NAS).", "chr_id": "1", "chr_pos": "91316444", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G949", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.980.980", "start_pos": 980, "end_pos": 980, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2PYH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DARELELILNRHPPFGTQIK", "down_seq": "TVMYLPKYELKVEQITRYSD", "snv": [ { "evidence": [ { "id": "A2PYH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2PYH4" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "91316145", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E980", "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:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "A2PYH4-1.999.999", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2PYH4-1.999.999", "start_pos": 999, "end_pos": 999, "uniprot_canonical_ac": "A2PYH4-1", "length": 1435, "uniprot_id": "HFM1_HUMAN", "protein_name": "Probable ATP-dependent DNA helicase HFM1", "refseq_ac": "NP_001017975", "refseq_name": "probable ATP-dependent DNA helicase HFM1", "gene_name": "HFM1", "gene_names_uniprotkb": "HFM1; SEC3D1", "gene_names_refseq": "HFM1; MER3; POF9; SEC63D1; Si-11-6; Si-11; helicase", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2PYH4", "url": "https://www.uniprot.org/uniprotkb/A2PYH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764012513", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764012513", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764012513", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764012513", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764012513", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764012513", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KETVMYLPKYELKVEQITRY", "down_seq": "DTTAEILVTVILRNFEQLQT", "snv": [ { "evidence": [ { "id": "rs764012513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764012513" }, { "id": "rs764012513", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764012513" }, { "id": "rs764012513", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764012513" } ], "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 (SDT->NDT).", "chr_id": "1", "chr_pos": "91315959", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S999", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1105", "end_pos": "1105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1002", "end_pos": "1002" }, { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" }, { "start_pos": "1176", "end_pos": "1176" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1292", "end_pos": "1292" }, { "start_pos": "1301", "end_pos": "1301" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "835", "end_pos": "835" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "980", "end_pos": "980" }, { "start_pos": "999", "end_pos": "999" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "A2PYH4-1.980.980", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "A2PYH4-1.1002.1002", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.1037.1037", "start_pos": 1037, "end_pos": 1037, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "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": "rs777536474", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777536474", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777536474", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777536474", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777536474", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777536474#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777536474", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777536474", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YQLELVNRETNFNKVFNSSP", "down_seq": "VGVINPLAKQKKKNDKSPTN", "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": "Thr1037", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs777536474", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777536474" }, { "id": "rs777536474", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777536474" }, { "id": "rs777536474", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777536474#frequency_tab" }, { "id": "rs777536474", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777536474" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "6", "chr_pos": "118964696", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1037", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q8NB25-1.1052.1052", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "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": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2114801925", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2114801925", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2114801925", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2114801925", "database": "1000Genomes", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MA", "down_seq": "PGMSWQQHYYGGSAAKFAPS", "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": "Thr3", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" }, { "id": "rs2114801925", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2114801925" }, { "id": "rs2114801925", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2114801925" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "6", "chr_pos": "119078292", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T3", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8NB25-1.0.0", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "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": "Q8NB25", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NB25" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NB25", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NB25", "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": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q8NB25", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NB25" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8NB25-1.3.3", "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" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 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": "Q8NB25-1.1052.1052", "start_pos": 1052, "end_pos": 1052, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FNSSPTVGVINPLAKQKKKN", "down_seq": "KSPTNRFVSVPNLSALESGG", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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 (DKS->NKS).", "chr_id": "6", "chr_pos": "118961948", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1052", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NB25-1.1037.1037", "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": "Q8NB25-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1785563712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785563712", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1785563712", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1785563712", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KHRVEDMQLCAEAQHVQRIV", "down_seq": "MSREVEEIRRKFEEKLRSFG", "snv": [ { "evidence": [ { "id": "rs1785563712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785563712" }, { "id": "rs1785563712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1785563712" } ], "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 (TMS->NMS).", "chr_id": "6", "chr_pos": "119024515", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T153", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8NB25-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NB25-1.170.170", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MQLCAEAQHVQRIVTMSREV", "down_seq": "EIRRKFEEKLRSFGQLQVQF", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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 (4).", "chr_id": "6", "chr_pos": "119024498", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E159", "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" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NB25-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NB25-1.170.170", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RIVTMSREVEEIRRKFEEKL", "down_seq": "SFGQLQVQFEKDKRLALEDL", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "119024464", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R170", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NB25-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NB25-1.159.159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1785556772", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785556772", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1785556772", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1785556772#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1785556772", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1785556772", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LEDLQAAHRREIQELLKSQQ", "down_seq": "HSASVNKGQEKAEELHRMEV", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" }, { "id": "rs1785556772", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785556772" }, { "id": "rs1785556772", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1785556772#frequency_tab" }, { "id": "rs1785556772", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1785556772" } ], "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 (DHS->NHS).", "chr_id": "6", "chr_pos": "119024354", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D207", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8NB25-1.215.215", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1785555873", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785555873", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1785555873", "url": "https://www.ensembl.org/id/rs1785555873", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RREIQELLKSQQDHSASVNK", "down_seq": "QEKAEELHRMEVESLNKMLE", "snv": [ { "evidence": [ { "id": "rs1785555873", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785555873" }, { "id": "rs1785555873", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1785555873" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKG->NKS).", "chr_id": "6", "chr_pos": "119024330", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G215", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NB25-1.207.207", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.299.299", "start_pos": 299, "end_pos": 299, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ASKEKEADLRKEFQGQEAIL", "down_seq": "KTIGKLKTELQMVQDEAGSL", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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 (6).", "chr_id": "6", "chr_pos": "119024077", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R299", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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" } ] }, { "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2535012866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2535012866", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TIGKLKTELQMVQDEAGSLL", "down_seq": "KCQKLQTALAIAENNVQVLQ", "snv": [ { "evidence": [ { "id": "rs2535012866", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2535012866" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKC->NKC).", "chr_id": "6", "chr_pos": "119024012", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D321", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YGGSAAKFAPSPATAQLAGH", "down_seq": "MDYSQEMHLKMSKKIAQLTK", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "119078202", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S33", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8NB25-1.35.35", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GSAAKFAPSPATAQLAGHSM", "down_seq": "YSQEMHLKMSKKIAQLTKVI", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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 (DYS->NYS).", "chr_id": "6", "chr_pos": "119078197", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D35", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8NB25-1.33.33", "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": "Q8NB25-1.413.413", "start_pos": 413, "end_pos": 413, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372823466", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372823466", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372823466", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372823466", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372823466", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372823466#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372823466", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372823466", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QMTQEVTIKDLESEKSRVNE", "down_seq": "LSQLEEERAFLRSKTQSLDE", "snv": [ { "evidence": [ { "id": "rs372823466", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372823466" }, { "id": "rs372823466", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372823466" }, { "id": "rs372823466", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372823466#frequency_tab" }, { "id": "rs372823466", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372823466" } ], "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": "6", "chr_pos": "119020071", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R413", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q8NB25-1.425.425", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.425.425", "start_pos": 425, "end_pos": 425, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SEKSRVNERLSQLEEERAFL", "down_seq": "SKTQSLDEEQKQQILELEKK", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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": "6", "chr_pos": "119020037", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R425", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NB25-1.413.413", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747503351", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747503351", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747503351", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747503351", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747503351", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747503351#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747503351", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747503351", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QSLDEEQKQQILELEKKVNE", "down_seq": "KRTQQEYYERELKNLQSRLE", "snv": [ { "evidence": [ { "id": "rs747503351", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747503351" }, { "id": "rs747503351", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747503351" }, { "id": "rs747503351", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747503351#frequency_tab" }, { "id": "rs747503351", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747503351" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEA->NET).", "chr_id": "6", "chr_pos": "119016932", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A449", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8NB25-1.450.450", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.450.450", "start_pos": 450, "end_pos": 450, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1785276540", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785276540", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1785276540", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1785276540#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SLDEEQKQQILELEKKVNEA", "down_seq": "RTQQEYYERELKNLQSRLEE", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" }, { "id": "rs1785276540", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785276540" }, { "id": "rs1785276540", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1785276540#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KRT->NRT).", "chr_id": "6", "chr_pos": "119016927", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K450", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8NB25-1.449.449", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.478.478", "start_pos": 478, "end_pos": 478, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749979020", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749979020", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749979020", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749979020", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749979020", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749979020", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ERELKNLQSRLEEEVTQLNE", "down_seq": "HSKTLEELAWKHHMAIEAVH", "snv": [ { "evidence": [ { "id": "rs749979020", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749979020" }, { "id": "rs749979020", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749979020" }, { "id": "rs749979020", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749979020" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEA->NES).", "chr_id": "6", "chr_pos": "119016845", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A478", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.503.503", "start_pos": 503, "end_pos": 503, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LEELAWKHHMAIEAVHSNAI", "down_seq": "DKKKLQMDLEEQHNKDKLNL", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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": "6", "chr_pos": "119016768", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R503", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q8NB25-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1472947042", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1472947042", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1472947042", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1472947042#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HLKMSKKIAQLTKVIYALNT", "down_seq": "NDEHESAIQALKDAHEEEIQ", "snv": [ { "evidence": [ { "id": "rs1472947042", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1472947042" }, { "id": "rs1472947042", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1472947042#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTK->NTT).", "chr_id": "6", "chr_pos": "119024791", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K61", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.646.646", "start_pos": 646, "end_pos": 646, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs188755585", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188755585", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs188755585", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188755585", "database": "1000Genomes", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EKLKVDKMAHDLEIKWTENL", "down_seq": "QECSKLREELRLQHEEDKKS", "snv": [ { "evidence": [ { "id": "rs188755585", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188755585" }, { "id": "rs188755585", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188755585" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLR->NLS).", "chr_id": "6", "chr_pos": "119003049", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R646", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q8NB25-1.664.664", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.664.664", "start_pos": 664, "end_pos": 664, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NLRQECSKLREELRLQHEED", "down_seq": "KSAMSQLLQLKDREKNAARD", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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 (KKS->NKS).", "chr_id": "6", "chr_pos": "119002995", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K664", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NB25-1.646.646", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NB25-1.682.682", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.682.682", "start_pos": 682, "end_pos": 682, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778598852", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778598852", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778598852", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778598852", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778598852", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778598852#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778598852", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778598852", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EDKKSAMSQLLQLKDREKNA", "down_seq": "RDSWQKKVEDLLNQISLLKQ", "snv": [ { "evidence": [ { "id": "rs778598852", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778598852" }, { "id": "rs778598852", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778598852" }, { "id": "rs778598852", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778598852#frequency_tab" }, { "id": "rs778598852", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778598852" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAA->NAS).", "chr_id": "6", "chr_pos": "119002943", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A682", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778598852", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778598852" }, { "id": "rs778598852", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778598852" }, { "id": "rs778598852", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778598852#frequency_tab" }, { "id": "rs778598852", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778598852" } ], "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": "6", "chr_pos": "119002943", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A682", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NB25-1.664.664", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "Q8NB25-1.723.723", "start_pos": 723, "end_pos": 723, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NLEIQLSQSQTSLQQLQAQF", "down_seq": "QERQRLTQELEELEEQHQQR", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "6", "chr_pos": "118980271", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T723", "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: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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8NB25-1.726.726", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NB25-1.730.730", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.726.726", "start_pos": 726, "end_pos": 726, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IQLSQSQTSLQQLQAQFTQE", "down_seq": "QRLTQELEELEEQHQQRHKS", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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": "6", "chr_pos": "118980263", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R726", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8NB25-1.723.723", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NB25-1.730.730", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NB25-1.744.744", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.730.730", "start_pos": 730, "end_pos": 730, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QSQTSLQQLQAQFTQERQRL", "down_seq": "QELEELEEQHQQRHKSLKEA", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "6", "chr_pos": "118980250", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T730", "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" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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: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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8NB25-1.723.723", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NB25-1.726.726", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NB25-1.744.744", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.744.744", "start_pos": 744, "end_pos": 744, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs77196341", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs77196341", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs77196341", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs77196341", "database": "1000Genomes", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "QERQRLTQELEELEEQHQQR", "down_seq": "KSLKEAHVLAFQTMEEEKEK", "snv": [ { "evidence": [ { "id": "rs77196341", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs77196341" }, { "id": "rs77196341", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs77196341" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HKS->NKS).", "chr_id": "6", "chr_pos": "118980209", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "H744", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NB25-1.726.726", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NB25-1.730.730", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.773.773", "start_pos": 773, "end_pos": 773, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1359731984", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359731984", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1359731984", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359731984", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LAFQTMEEEKEKEQRALENH", "down_seq": "QQKHSAELQSLKDAHRESME", "snv": [ { "evidence": [ { "id": "rs1359731984", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359731984" }, { "id": "rs1359731984", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359731984" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHL->NHS).", "chr_id": "6", "chr_pos": "118979502", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L773", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.816.816", "start_pos": 816, "end_pos": 816, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RIEMEQELQTLRFELEDEGK", "down_seq": "MLASLRSELNHQHAAAIDLL", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "118979373", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A816", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8NB25-1.822.822", "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": "Q8NB25-1.822.822", "start_pos": 822, "end_pos": 822, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELQTLRFELEDEGKAMLASL", "down_seq": "SELNHQHAAAIDLLRHNHHQ", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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": "6", "chr_pos": "118976035", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R822", "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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NB25-1.816.816", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NB25-1.837.837", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.837.837", "start_pos": 837, "end_pos": 837, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NB25", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MLASLRSELNHQHAAAIDLL", "down_seq": "HNHHQELAAAKMELERSIDI", "snv": [ { "evidence": [ { "id": "Q8NB25", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NB25" } ], "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 (4).", "chr_id": "6", "chr_pos": "118975991", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R837", "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: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": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NB25-1.822.822", "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": "Q8NB25-1.951.951", "start_pos": 951, "end_pos": 951, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1253914864", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1253914864", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1253914864", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1253914864#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1253914864", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1253914864", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KRLEKELDVMTADHLREKNI", "down_seq": "RADFNKTNELLKEINAALQV", "snv": [ { "evidence": [ { "id": "rs1253914864", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1253914864" }, { "id": "rs1253914864", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1253914864#frequency_tab" }, { "id": "rs1253914864", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1253914864" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIM->NIT).", "chr_id": "6", "chr_pos": "118974491", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M951", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q8NB25-1.968.968", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.968.968", "start_pos": 968, "end_pos": 968, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778308463", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778308463", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778308463", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778308463", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778308463", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778308463#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778308463", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778308463", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KNIMRADFNKTNELLKEINA", "down_seq": "LQVSLEEMEEKYLMRESKPE", "snv": [ { "evidence": [ { "id": "rs778308463", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778308463" }, { "id": "rs778308463", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778308463" }, { "id": "rs778308463", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778308463#frequency_tab" }, { "id": "rs778308463", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778308463" } ], "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": "6", "chr_pos": "118974441", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A968", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NB25-1.951.951", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NB25-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "Q8NB25-1", "length": 1140, "uniprot_id": "F184A_HUMAN", "protein_name": "Protein FAM184A", "refseq_ac": "NP_001275505", "refseq_name": "protein FAM184A isoform 3", "gene_name": "FAM184A", "gene_names_uniprotkb": "FAM184A; C6orf60", "gene_names_refseq": "C6orf60; FAM184A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NB25", "url": "https://www.uniprot.org/uniprotkb/Q8NB25" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1228425793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1228425793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1228425793", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1228425793#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1785568793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785568793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1785568793", "url": "https://www.ensembl.org/id/rs1785568793", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EEEIQQILAETREKILQYKS", "down_seq": "VTEELDLRRKIQVLESSLED", "snv": [ { "evidence": [ { "id": "rs1228425793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1228425793" }, { "id": "rs1228425793", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1228425793#frequency_tab" }, { "id": "rs1785568793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1785568793" }, { "id": "rs1785568793", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1785568793" } ], "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": "6", "chr_pos": "119024684_119024685insTATACTGCAAT", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K97", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1052", "end_pos": "1052" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "837", "end_pos": "837" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IV04-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "Q8IV04-1", "length": 446, "uniprot_id": "TB10C_HUMAN", "protein_name": "Carabin", "refseq_ac": "NP_001243437", "refseq_name": "carabin isoform 2", "gene_name": "TBC1D10C", "gene_names_uniprotkb": "TBC1D10C", "gene_names_refseq": "CARABIN; EPI64C; TBC1D10C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Feedback inhibition of calcineurin and Ras by a dual inhibitory protein Carabin.", "journal": "Nature", "date": "2007", "authors": "Pan F, Sun L, Kardian DB, Whartenby KA, Pardoll DM, Liu JO", "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" }, { "database": "RefSeq", "id": "NP_001243437", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001243437" } ], "reference": [ { "type": "PubMed", "id": "17230191", "url": "https://glygen.org/publication/PubMed/17230191" } ] } ], "crossref": [ { "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17230191", "url": "https://glygen.org/publication/PubMed/17230191", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELAEAPGDPQWMETIGRDLH", "down_seq": "QFPLHEMFVSPQGHGQQGLL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Loss of GAP activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" }, { "database": "PubMed", "id": "17230191", "url": "https://glygen.org/publication/PubMed/17230191" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "141", "end_pos": "141" } ] }, { "type": "snv", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "321", "end_pos": "321" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" } ] } ], "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": "Q8IV04-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q8IV04-1", "length": 446, "uniprot_id": "TB10C_HUMAN", "protein_name": "Carabin", "refseq_ac": "NP_001243437", "refseq_name": "carabin isoform 2", "gene_name": "TBC1D10C", "gene_names_uniprotkb": "TBC1D10C", "gene_names_refseq": "CARABIN; EPI64C; TBC1D10C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IV04", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV04", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SPQGHGQQGLLQVLKAYTLY", "down_seq": "PEQGYCQAQGPVAAVLLMHL", "snv": [ { "evidence": [ { "id": "Q8IV04", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV04" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "67405946", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R171", "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "141", "end_pos": "141" } ] }, { "type": "snv", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "321", "end_pos": "321" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IV04-1.316.316", "start_pos": 316, "end_pos": 316, "uniprot_canonical_ac": "Q8IV04-1", "length": 446, "uniprot_id": "TB10C_HUMAN", "protein_name": "Carabin", "refseq_ac": "NP_001243437", "refseq_name": "carabin isoform 2", "gene_name": "TBC1D10C", "gene_names_uniprotkb": "TBC1D10C", "gene_names_refseq": "CARABIN; EPI64C; TBC1D10C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IV04", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV04", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LGTAEQRGACPGLLETLGAL", "down_seq": "AIPPAQLQEEAFMSQVHSVV", "snv": [ { "evidence": [ { "id": "Q8IV04", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV04" } ], "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": "11", "chr_pos": "67409087", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R316", "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": "mutagenesis", "site_list": [ { "start_pos": "141", "end_pos": "141" } ] }, { "type": "snv", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "321", "end_pos": "321" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8IV04-1.321.321", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IV04-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "Q8IV04-1", "length": 446, "uniprot_id": "TB10C_HUMAN", "protein_name": "Carabin", "refseq_ac": "NP_001243437", "refseq_name": "carabin isoform 2", "gene_name": "TBC1D10C", "gene_names_uniprotkb": "TBC1D10C", "gene_names_refseq": "CARABIN; EPI64C; TBC1D10C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IV04", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV04", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QRGACPGLLETLGALRAIPP", "down_seq": "QLQEEAFMSQVHSVVLSERD", "snv": [ { "evidence": [ { "id": "Q8IV04", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IV04" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "67409102", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A321", "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: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": "141", "end_pos": "141" } ] }, { "type": "snv", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "321", "end_pos": "321" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8IV04-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IV04-1.438.438", "start_pos": 438, "end_pos": 438, "uniprot_canonical_ac": "Q8IV04-1", "length": 446, "uniprot_id": "TB10C_HUMAN", "protein_name": "Carabin", "refseq_ac": "NP_001243437", "refseq_name": "carabin isoform 2", "gene_name": "TBC1D10C", "gene_names_uniprotkb": "TBC1D10C", "gene_names_refseq": "CARABIN; EPI64C; TBC1D10C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q8IV04-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV04-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "Q8IV04", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV04", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLLTRARGPPIEGPPRPQRG", "down_seq": "TSFLDTRF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8IV04", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV04" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Ser438" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "141", "end_pos": "141" } ] }, { "type": "snv", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "321", "end_pos": "321" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8IV04-1.439.439", "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": "Q8IV04-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "Q8IV04-1", "length": 446, "uniprot_id": "TB10C_HUMAN", "protein_name": "Carabin", "refseq_ac": "NP_001243437", "refseq_name": "carabin isoform 2", "gene_name": "TBC1D10C", "gene_names_uniprotkb": "TBC1D10C", "gene_names_refseq": "CARABIN; EPI64C; TBC1D10C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IV04", "url": "https://www.uniprot.org/uniprotkb/Q8IV04" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q8IV04-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV04-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "Q8IV04", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV04", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLTRARGPPIEGPPRPQRGS", "down_seq": "SFLDTRF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8IV04", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IV04" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Thr439" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "141", "end_pos": "141" } ] }, { "type": "snv", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "321", "end_pos": "321" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8IV04-1.438.438", "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": "P08397-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "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": "P08397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08397" } ], "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": "P08397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08397" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P08397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08397" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P08397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08397", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "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": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P08397", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08397" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P08397-1.15.15", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P08397-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into acute intermittent porphyria.", "journal": "FASEB journal : official publication of the Federation of American Societies for Experimental Biology", "date": "2009", "authors": "Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "reference": [ { "type": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "crossref": [ { "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LPTVLPPGFTIGAICKRENP", "down_seq": "DAVVFHPKFVGKTLETLPEK", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Decreased hydroxymethylbilane synthase activity.", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] }, { "sequence_org": "H", "sequence_mut": "P", "comment": "Loss of hydroxymethylbilane synthase activity.", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "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": "P08397-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into acute intermittent porphyria.", "journal": "FASEB journal : official publication of the Federation of American Societies for Experimental Biology", "date": "2009", "authors": "Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "reference": [ { "type": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "crossref": [ { "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RKLDEQQEFSAIILATAGLQ", "down_seq": "MGWHNRVGQILHPEECMYAV", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Loss of hydroxymethylbilane synthase activity.", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P08397-1.175.175", "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": "P08397-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into acute intermittent porphyria.", "journal": "FASEB journal : official publication of the Federation of American Societies for Experimental Biology", "date": "2009", "authors": "Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "reference": [ { "type": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "crossref": [ { "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NAAATAEENSPKMRVIRVGT", "down_seq": "KSQLARIQTDSVVATLKASY", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Loss of hydroxymethylbilane synthase activity.", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P08397-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P08397-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P08397-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P08397-1.34.34", "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": "P08397-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into acute intermittent porphyria.", "journal": "FASEB journal : official publication of the Federation of American Societies for Experimental Biology", "date": "2009", "authors": "Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "reference": [ { "type": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "crossref": [ { "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "NSPKMRVIRVGTRKSQLARI", "down_seq": "TDSVVATLKASYPGLQFEII", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Loss of hydroxymethylbilane synthase activity.", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "18936296", "url": "https://glygen.org/publication/PubMed/18936296" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P08397-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P08397-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P08397-1.26.26", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P08397-1.32.32", "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": "P08397-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QRKFPHLEFRSIRGNLNTRL", "down_seq": "KLDEQQEFSAIILATAGLQR", "snv": [ { "evidence": [ { "id": "P08397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397" } ], "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": "11", "chr_pos": "119091437", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R175", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "P08397-1.195.195", "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": "P08397-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SGNGNAAATAEENSPKMRVI", "down_seq": "VGTRKSQLARIQTDSVVATL", "snv": [ { "evidence": [ { "id": "P08397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397" } ], "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": "11", "chr_pos": "119088285", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R22", "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": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P08397-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P08397-1.26.26", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P08397-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P08397-1.34.34", "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": "P08397-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VEVRAKDQDILDLVGVLHDP", "down_seq": "TLLRCIAERAFLRHLEGGCS", "snv": [ { "evidence": [ { "id": "P08397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397" } ], "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": "11", "chr_pos": "119092476", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E242", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P08397-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P08397-1.249.249", "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": "P08397-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AKDQDILDLVGVLHDPETLL", "down_seq": "CIAERAFLRHLEGGCSVPVA", "snv": [ { "evidence": [ { "id": "P08397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "119092489", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R246", "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": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P08397-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P08397-1.249.249", "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": "P08397-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QDILDLVGVLHDPETLLRCI", "down_seq": "ERAFLRHLEGGCSVPVAVHT", "snv": [ { "evidence": [ { "id": "P08397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "119092497", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A249", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P08397-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P08397-1.246.246", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P08397-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VPAQHEDGPEDDPQLVGITA", "down_seq": "NIPRGPQLAAQNLGISLANL", "snv": [ { "evidence": [ { "id": "P08397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "119093158", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R321", "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" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "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": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P08397-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EENSPKMRVIRVGTRKSQLA", "down_seq": "IQTDSVVATLKASYPGLQFE", "snv": [ { "evidence": [ { "id": "P08397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08397" } ], "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": "119088642", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R32", "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": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P08397-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P08397-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P08397-1.26.26", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P08397-1.34.34", "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": "P08397-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "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": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "iPTMnet", "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PKFVGKTLETLPEKSVVGTS", "down_seq": "LRRAAQLQRKFPHLEFRSIR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397" } ], "site_lbl": "Ser147" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "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": "P08397-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "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": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "iPTMnet", "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "P08397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397", "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": "MSGNGNAAATAEEN", "down_seq": "PKMRVIRVGTRKSQLARIQT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser15" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P08397-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P08397-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P08397-1.26.26", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P08397-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P08397-1.34.34", "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": "P08397-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P08397-1", "length": 361, "uniprot_id": "HEM3_HUMAN", "protein_name": "Porphobilinogen deaminase", "refseq_ac": "NP_000181", "refseq_name": "porphobilinogen deaminase isoform 1", "gene_name": "HMBS", "gene_names_uniprotkb": "HMBS; PBGD; UPS", "gene_names_refseq": "ENCEP; HMBS; LENCEP; PBG-D; PBGD; PORC; UPS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" } ], "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": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "iPTMnet", "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQFEIIAMSTTGDKILDTAL", "down_seq": "KIGEKSLFTKELEHALEKNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P08397", "url": "https://www.uniprot.org/uniprotkb/P08397" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P08397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P08397" } ], "site_lbl": "Ser69" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "120", "end_pos": "120" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "34", "end_pos": "34" } ] }, { "type": "snv", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "69", "end_pos": "69" } ] } ], "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": "O60921-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O60921-1", "length": 280, "uniprot_id": "HUS1_HUMAN", "protein_name": "Checkpoint protein HUS1", "refseq_ac": "NP_004498", "refseq_name": "checkpoint protein HUS1 isoform 1", "gene_name": "HUS1", "gene_names_uniprotkb": "HUS1", "gene_names_refseq": "HUS1; hHUS1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60921", "url": "https://www.uniprot.org/uniprotkb/O60921" } ], "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": "O60921", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60921" } ], "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": "O60921", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60921", "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": "O60921", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60921" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O60921-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "O60921-1", "length": 280, "uniprot_id": "HUS1_HUMAN", "protein_name": "Checkpoint protein HUS1", "refseq_ac": "NP_004498", "refseq_name": "checkpoint protein HUS1 isoform 1", "gene_name": "HUS1", "gene_names_uniprotkb": "HUS1", "gene_names_refseq": "HUS1; hHUS1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60921", "url": "https://www.uniprot.org/uniprotkb/O60921" } ], "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": "O60921-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60921-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "O60921", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60921", "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": "IEANLDGELNLKIETELVCV", "down_seq": "THFKDLGNPPLASESTHEDR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O60921", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60921" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Thr202" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q658Y4-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q658Y4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "Q658Y4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "crossref": [ { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q658Y4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q658Y4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "Q658Y4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q658Y4" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "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": "Q658Y4-1.377.377", "start_pos": 377, "end_pos": 377, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q658Y4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EDPADTASVSSLSLSTGHTK", "down_seq": "IAFLFDSTLTAFLMMGNLSP", "snv": [ { "evidence": [ { "id": "Q658Y4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4" } ], "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": "8", "chr_pos": "123787312", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R377", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q658Y4-1.364.364", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q658Y4-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q658Y4-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q658Y4-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q658Y4-1.379.379", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q658Y4-1.379.379", "start_pos": 379, "end_pos": 379, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q658Y4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PADTASVSSLSLSTGHTKRI", "down_seq": "FLFDSTLTAFLMMGNLSPNL", "snv": [ { "evidence": [ { "id": "Q658Y4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "8", "chr_pos": "123787317", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A379", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID: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": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q658Y4-1.364.364", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q658Y4-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q658Y4-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q658Y4-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q658Y4-1.377.377", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q658Y4-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q658Y4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GEAQRYFDHALTLRNTILFL", "down_seq": "HNKDLVAQTAQPDQPNYGFP", "snv": [ { "evidence": [ { "id": "Q658Y4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "123789692", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R453", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID: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": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q658Y4-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q658Y4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ATCSRVLNKNYTLLVSMAPL", "down_seq": "NEIRPVSSCTPQHIGPAIPE", "snv": [ { "evidence": [ { "id": "Q658Y4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4" } ], "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: num. of cancers (3).", "chr_id": "8", "chr_pos": "123798200", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T508", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q658Y4-1.512.512", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q658Y4-1.512.512", "start_pos": 512, "end_pos": 512, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q658Y4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RVLNKNYTLLVSMAPLTNEI", "down_seq": "PVSSCTPQHIGPAIPEVSSV", "snv": [ { "evidence": [ { "id": "Q658Y4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4" } ], "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": "8", "chr_pos": "123798213", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R512", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q658Y4-1.508.508", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q658Y4-1.558.558", "start_pos": 558, "end_pos": 558, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q658Y4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IYHVTGQGPPSLLLSKGTRL", "down_seq": "KLPDIFQSYDRLLITSWGHD", "snv": [ { "evidence": [ { "id": "Q658Y4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "123799631", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R558", "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" ] }, { "evidence": [ { "id": "Q658Y4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q658Y4" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "8", "chr_pos": "123799632", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R558", "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": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q658Y4-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KNVPSVNRLKSTLDPQKMLL", "down_seq": "WDGGESRSPVQEASSATDTD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "site_lbl": "Ser332" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q658Y4-1.340.340", "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": "Q658Y4-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4", "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": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKSTLDPQKMLLSWDGGESR", "down_seq": "PVQEASSATDTDTNSQEDPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "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": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "site_lbl": "Ser340" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q658Y4-1.332.332", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q658Y4-1.355.355", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q658Y4-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGESRSPVQEASSATDTDTN", "down_seq": "QEDPADTASVSSLSLSTGHT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser355" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q658Y4-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q658Y4-1.364.364", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q658Y4-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q658Y4-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q658Y4-1.371.371", "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": "Q658Y4-1.364.364", "start_pos": 364, "end_pos": 364, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "EASSATDTDTNSQEDPADTA", "down_seq": "VSSLSLSTGHTKRIAFLFDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser364" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q658Y4-1.355.355", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q658Y4-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q658Y4-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q658Y4-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q658Y4-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q658Y4-1.379.379", "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": "Q658Y4-1.366.366", "start_pos": 366, "end_pos": 366, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "SSATDTDTNSQEDPADTASV", "down_seq": "SLSLSTGHTKRIAFLFDSTL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser366" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q658Y4-1.355.355", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q658Y4-1.364.364", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q658Y4-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q658Y4-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q658Y4-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q658Y4-1.379.379", "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": "Q658Y4-1.367.367", "start_pos": 367, "end_pos": 367, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "SATDTDTNSQEDPADTASVS", "down_seq": "LSLSTGHTKRIAFLFDSTLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser367" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q658Y4-1.355.355", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q658Y4-1.364.364", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q658Y4-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q658Y4-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q658Y4-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q658Y4-1.379.379", "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": "Q658Y4-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TDTNSQEDPADTASVSSLSL", "down_seq": "TGHTKRIAFLFDSTLTAFLM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ], "site_lbl": "Ser371" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q658Y4-1.355.355", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q658Y4-1.364.364", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q658Y4-1.366.366", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q658Y4-1.367.367", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q658Y4-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q658Y4-1.379.379", "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": "Q658Y4-1.671.671", "start_pos": 671, "end_pos": 671, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLCGYVTMLNASSQLADRKL", "down_seq": "DASDERGEPDLASGSDVNGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser671" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q658Y4-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q658Y4-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q658Y4-1.691.691", "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": "Q658Y4-1.674.674", "start_pos": 674, "end_pos": 674, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "GYVTMLNASSQLADRKLSDA", "down_seq": "DERGEPDLASGSDVNGSTES", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser674" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q658Y4-1.671.671", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q658Y4-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q658Y4-1.691.691", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q658Y4-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q658Y4-1.684.684", "start_pos": 684, "end_pos": 684, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "QLADRKLSDASDERGEPDLA", "down_seq": "GSDVNGSTESFEMVIEEATI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser684" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q658Y4-1.671.671", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q658Y4-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q658Y4-1.691.691", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q658Y4-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q658Y4-1.691.691", "start_pos": 691, "end_pos": 691, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "SDASDERGEPDLASGSDVNG", "down_seq": "TESFEMVIEEATIDSATKQT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser691" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q658Y4-1.671.671", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q658Y4-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q658Y4-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q658Y4-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q658Y4-1.692.692", "start_pos": 692, "end_pos": 692, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "DASDERGEPDLASGSDVNGS", "down_seq": "ESFEMVIEEATIDSATKQTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Thr692" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q658Y4-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q658Y4-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q658Y4-1.691.691", "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": "Q658Y4-1.826.826", "start_pos": 826, "end_pos": 826, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "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": "PLPAKNLIFKDGVLSEWSGR", "down_seq": "PSSLLIANLHLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser826" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q658Y4-1.828.828", "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": "Q658Y4-1.828.828", "start_pos": 828, "end_pos": 828, "uniprot_canonical_ac": "Q658Y4-1", "length": 838, "uniprot_id": "F91A1_HUMAN", "protein_name": "Protein FAM91A1", "refseq_ac": "NP_001304847", "refseq_name": "protein FAM91A1 isoform 3", "gene_name": "FAM91A1", "gene_names_uniprotkb": "FAM91A1", "gene_names_refseq": "FAM91A1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" } ], "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": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PAKNLIFKDGVLSEWSGRSP", "down_seq": "SLLIANLHLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q658Y4", "url": "https://www.uniprot.org/uniprotkb/Q658Y4" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q658Y4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q658Y4" } ], "site_lbl": "Ser828" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "377", "end_pos": "377" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "558", "end_pos": "558" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "332", "end_pos": "332" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "691", "end_pos": "691" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "828", "end_pos": "828" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q658Y4-1.826.826", "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": "Q96MK3-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q96MK3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1600580753", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600580753", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600580753", "url": "https://www.ensembl.org/id/rs1600580753", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1164700537", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1164700537", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YYRRKVARWNRRHKMYREQM", "down_seq": "LTSLDPPLQLRLEASWVQFH", "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": "Asn145", "evidence": [ { "id": "Q96MK3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q96MK3#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "Q96MK3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->DLT).", "chr_id": "17", "chr_pos": "68555715", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N145", "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": "rs1600580753", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600580753" }, { "id": "rs1600580753", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600580753" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->ILT).", "chr_id": "17", "chr_pos": "68555714", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1164700537", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1164700537" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->KLT).", "chr_id": "17", "chr_pos": "68555713", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1600580753", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600580753" }, { "id": "rs1600580753", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600580753" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->TLT).", "chr_id": "17", "chr_pos": "68555714", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q96MK3-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q96MK3-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96MK3-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q96MK3-1.148.148", "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": 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": "Q96MK3-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "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": "rs1600580702", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600580702", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600580702", "url": "https://www.ensembl.org/id/rs1600580702", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKVARWNRRHKMYREQMNLT", "down_seq": "LDPPLQLRLEASWVQFHLGI", "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": "Ser148", "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": "rs1600580702", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600580702" }, { "id": "rs1600580702", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600580702" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "17", "chr_pos": "68555706", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S148", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q96MK3-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q96MK3-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96MK3-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q96MK3-1.147.147", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96MK3-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "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": "NAEIAAFHLDRILDFRRVPP", "down_seq": "VGRIVNVTKEILEVTKNEIL", "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": "Thr281", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q96MK3-1.287.287", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q96MK3-1.300.300", "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": "Q96MK3-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FHLDRILDFRRVPPTVGRIV", "down_seq": "VTKEILEVTKNEILQSVFFV", "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": "Asn287", "evidence": [ { "id": "Q96MK3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q96MK3#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q96MK3-1.281.281", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q96MK3-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q96MK3-1.305.305", "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": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "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": "rs2086360616", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2086360616", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2086360616", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2086360616", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VTKEILEVTKNEILQSVFFV", "down_seq": "PASNVCFFAKCPYMCKTEYA", "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": "Ser308", "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": "rs2086360616", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2086360616" }, { "id": "rs2086360616", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2086360616" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "17", "chr_pos": "68542699", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S308", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q96MK3-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q96MK3-1.305.305", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96MK3-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "5WRR", "url": "https://www.rcsb.org/structure/5WRR", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "5WRS", "url": "https://www.rcsb.org/structure/5WRS", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "5WRR|B|388", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5WRS|B|388", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5WRS|A|388", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs776028847", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776028847", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776028847", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776028847", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776028847", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776028847", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KEEWEVNPLYCDTVKQIYPY", "down_seq": "NSQRLLNVIDMAIFDFLIGN", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=5WRR&bu=0&command=select+.B:388;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn388", "evidence": [ { "id": "Q96MK3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q96MK3#ptm_processing" }, { "id": "5WRR", "database": "PDB", "url": "https://www.rcsb.org/structure/5WRR" }, { "id": "5WRS", "database": "PDB", "url": "https://www.rcsb.org/structure/5WRS" } ] } ], "snv": [ { "evidence": [ { "id": "rs776028847", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776028847" }, { "id": "rs776028847", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776028847" }, { "id": "rs776028847", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776028847" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNS->SNS).", "chr_id": "17", "chr_pos": "68540905", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N388", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q96MK3-1.390.390", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q96MK3-1.400.400", "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", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.538.538", "start_pos": 538, "end_pos": 538, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1229691293", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229691293", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1229691293", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1229691293#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QQSVIVDGPVEQLAPDSGQA", "down_seq": "LTS", "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": "Asn538", "evidence": [ { "id": "Q96MK3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q96MK3#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1229691293", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229691293" }, { "id": "rs1229691293", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1229691293#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->KLT).", "chr_id": "17", "chr_pos": "68537489", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N538", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q96MK3-1.540.540", "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": "Q96MK3-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2088588651", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088588651", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2088588651", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2088588651", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ASSLARDSAAAASDPGTIVH", "down_seq": "FSRTEPRTEPAGGSHSGSSS", "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": "DSAAAASDPGTIVHnFSR", "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": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "Q96MK3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q96MK3#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2088588651", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088588651" }, { "id": "rs2088588651", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2088588651" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NFS->SFS).", "chr_id": "17", "chr_pos": "68600458", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N70", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "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": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96MK3-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A secretory kinase complex regulates extracellular protein phosphorylation.", "journal": "eLife", "date": "2015", "authors": "Cui J, Xiao J, Tagliabracci VS, Wen J, Rahdar M, Dixon JE", "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "reference": [ { "type": "PubMed", "id": "25789606", "url": "https://glygen.org/publication/PubMed/25789606" } ] } ], "crossref": [ { "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25789606", "url": "https://glygen.org/publication/PubMed/25789606", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PMRQQRDEETPVDFFYFIDF", "down_seq": "RHNAEIAAFHLDRILDFRRV", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "E", "comment": "Able to hydrolyze ATP and display some protein kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" }, { "database": "PubMed", "id": "25789606", "url": "https://glygen.org/publication/PubMed/25789606" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "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": "Q96MK3-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1349145345", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349145345", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1349145345", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349145345", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SHSGSSSKLQALFAHPLYNV", "down_seq": "EEPPLLGAEDSLLASQEALR", "snv": [ { "evidence": [ { "id": "rs1349145345", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349145345" }, { "id": "rs1349145345", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349145345" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVP->NVS).", "chr_id": "17", "chr_pos": "68600357", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLASQEALRYYRRKVARWNR", "down_seq": "HKMYREQMNLTSLDPPLQLR", "snv": [ { "evidence": [ { "id": "Q96MK3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "68555742", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R136", "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": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q96MK3-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q96MK3-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q96MK3-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q96MK3-1.148.148", "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": "Q96MK3-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs978270892", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978270892", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs978270892", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978270892#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "YRRKVARWNRRHKMYREQMN", "down_seq": "TSLDPPLQLRLEASWVQFHL", "snv": [ { "evidence": [ { "id": "rs978270892", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978270892" }, { "id": "rs978270892", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978270892#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NPT).", "chr_id": "17", "chr_pos": "68555711", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L146", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q96MK3-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q96MK3-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q96MK3-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96MK3-1.148.148", "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": "Q96MK3-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs145784842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145784842", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145784842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145784842", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145784842", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145784842#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145784842", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145784842", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1600580728", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600580728", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600580728", "url": "https://www.ensembl.org/id/rs1600580728", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RRKVARWNRRHKMYREQMNL", "down_seq": "SLDPPLQLRLEASWVQFHLG", "snv": [ { "evidence": [ { "id": "rs145784842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145784842" }, { "id": "rs145784842", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145784842" }, { "id": "rs145784842", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145784842#frequency_tab" }, { "id": "rs145784842", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145784842" } ], "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": "68555708", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T147", "disease": [ { "disease_id": "DOID:0110066", "recommended_name": { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta type 1G", "description": "An amelogenesis imperfecta that has_material_basis_in homozygous or compound heterozygous mutation in the FAM20A gene on chromosome 17q24." }, "synonyms": [ { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta and gingival fibromatosis syndrome", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta hypoplastic with nephrocalcinosis", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "AI1G", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "AIGFS", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "ERS", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta type IG", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "enamel-renal syndrome", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "enamel-renal-gingival syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta type 1G", "description": "An extremely rare syndrome which is characterized by hypoplastic amelogenesis imperfecta (hypoplastic dental enamel) and nephrocalcinosis (precipitation of calcium salts in renal tissue). Oral manifestations include yellow and misshaped teeth, delayed tooth eruption, and intrapulpal calcifications. Nephrocalcinosis is often asymptomatic but can progress during late childhood or early adulthood to impaired renal function (e.g. recurrent urinary infections and renal tubular acidosis), and rarely to end-stage renal failure." }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AI1G", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AIGFS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ERS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "FAM20A amelogenesis imperfecta", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and gingival fibromatosis syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta caused by mutation in FAM20A", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG (enamel-renal syndrome)", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta-gingival hyperplasia syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal-gingival syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ers", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "absent enamel, nephrocalcinosis and apparently normal calcium metabolism", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta hypoplastic type, IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalised enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalized enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta type 1G", "description": "An extremely rare syndrome which is characterized by hypoplastic amelogenesis imperfecta (hypoplastic dental enamel) and nephrocalcinosis (precipitation of calcium salts in renal tissue). Oral manifestations include yellow and misshaped teeth, delayed tooth eruption, and intrapulpal calcifications. Nephrocalcinosis is often asymptomatic but can progress during late childhood or early adulthood to impaired renal function (e.g. recurrent urinary infections and renal tubular acidosis), and rarely to end-stage renal failure." }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AI1G", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AIGFS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ERS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "FAM20A amelogenesis imperfecta", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and gingival fibromatosis syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta caused by mutation in FAM20A", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG (enamel-renal syndrome)", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta-gingival hyperplasia syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal-gingival syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ers", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "absent enamel, nephrocalcinosis and apparently normal calcium metabolism", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta hypoplastic type, IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalised enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalized enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MIM:204690", "resource": "MIM", "url": "https://www.omim.org/entry/204690", "name": "Amelogenesis imperfecta 1G", "description": "Amelogenesis imperfecta 1G" } ], "unlinked_id_list": [], "evidence": [ { "id": "204690", "database": "MIM", "url": "https://www.omim.org/entry/204690" }, { "id": "0110066", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0110066" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1600580728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600580728" }, { "id": "rs1600580728", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600580728" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLP).", "chr_id": "17", "chr_pos": "68555709", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T147", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q96MK3-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96MK3-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q96MK3-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q96MK3-1.148.148", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774517781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774517781", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774517781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774517781", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774517781", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774517781#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774517781", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774517781", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HFPTISADYSQDEKALLGAC", "down_seq": "CTQIVKPSGVHLKLVLRFSD", "snv": [ { "evidence": [ { "id": "rs774517781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774517781" }, { "id": "rs774517781", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774517781" }, { "id": "rs774517781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774517781#frequency_tab" }, { "id": "rs774517781", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774517781" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DCT->NCT).", "chr_id": "17", "chr_pos": "68554789", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D210", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372280569", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372280569", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372280569", "url": "https://www.ensembl.org/id/rs372280569", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "PTVGRIVNVTKEILEVTKNE", "down_seq": "LQSVFFVSPASNVCFFAKCP", "snv": [ { "evidence": [ { "id": "rs372280569", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372280569" }, { "id": "rs372280569", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs372280569" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEI->NET).", "chr_id": "17", "chr_pos": "68542723", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I300", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q96MK3-1.281.281", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q96MK3-1.287.287", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q96MK3-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q96MK3-1.308.308", "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": "Q96MK3-1.305.305", "start_pos": 305, "end_pos": 305, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "IVNVTKEILEVTKNEILQSV", "down_seq": "FVSPASNVCFFAKCPYMCKT", "snv": [ { "evidence": [ { "id": "Q96MK3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "68542707", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F305", "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": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q96MK3-1.287.287", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q96MK3-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q96MK3-1.308.308", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.350.350", "start_pos": 350, "end_pos": 350, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "CGNPHLLEGSLSAFLPSLNL", "down_seq": "PRLSVPNPWIRSYTLAGKEE", "snv": [ { "evidence": [ { "id": "Q96MK3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLT).", "chr_id": "17", "chr_pos": "68542046", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A350", "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": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.390.390", "start_pos": 390, "end_pos": 390, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775260607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775260607", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775260607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775260607", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775260607", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775260607#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775260607", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775260607", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs771912912", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771912912", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771912912", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771912912", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EWEVNPLYCDTVKQIYPYNN", "down_seq": "QRLLNVIDMAIFDFLIGNMD", "snv": [ { "evidence": [ { "id": "rs775260607", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775260607" }, { "id": "rs775260607", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775260607" }, { "id": "rs775260607", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775260607#frequency_tab" }, { "id": "rs775260607", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775260607" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNS->NNG).", "chr_id": "17", "chr_pos": "68540900", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S390", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771912912", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771912912" }, { "id": "rs771912912", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771912912" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNS->NNN).", "chr_id": "17", "chr_pos": "68540899", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S390", "disease": [ { "disease_id": "DOID:0110066", "recommended_name": { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta type 1G", "description": "An amelogenesis imperfecta that has_material_basis_in homozygous or compound heterozygous mutation in the FAM20A gene on chromosome 17q24." }, "synonyms": [ { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta and gingival fibromatosis syndrome", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta hypoplastic with nephrocalcinosis", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "AI1G", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "AIGFS", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "ERS", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "amelogenesis imperfecta type IG", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "enamel-renal syndrome", "description": "" }, { "id": "DOID:0110066", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110066", "name": "enamel-renal-gingival syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta type 1G", "description": "An extremely rare syndrome which is characterized by hypoplastic amelogenesis imperfecta (hypoplastic dental enamel) and nephrocalcinosis (precipitation of calcium salts in renal tissue). Oral manifestations include yellow and misshaped teeth, delayed tooth eruption, and intrapulpal calcifications. Nephrocalcinosis is often asymptomatic but can progress during late childhood or early adulthood to impaired renal function (e.g. recurrent urinary infections and renal tubular acidosis), and rarely to end-stage renal failure." }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AI1G", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AIGFS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ERS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "FAM20A amelogenesis imperfecta", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and gingival fibromatosis syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta caused by mutation in FAM20A", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG (enamel-renal syndrome)", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta-gingival hyperplasia syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal-gingival syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ers", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "absent enamel, nephrocalcinosis and apparently normal calcium metabolism", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta hypoplastic type, IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalised enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalized enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta type 1G", "description": "An extremely rare syndrome which is characterized by hypoplastic amelogenesis imperfecta (hypoplastic dental enamel) and nephrocalcinosis (precipitation of calcium salts in renal tissue). Oral manifestations include yellow and misshaped teeth, delayed tooth eruption, and intrapulpal calcifications. Nephrocalcinosis is often asymptomatic but can progress during late childhood or early adulthood to impaired renal function (e.g. recurrent urinary infections and renal tubular acidosis), and rarely to end-stage renal failure." }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AI1G", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "AIGFS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ERS", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "FAM20A amelogenesis imperfecta", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and gingival fibromatosis syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta caused by mutation in FAM20A", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG (enamel-renal syndrome)", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta-gingival hyperplasia syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel-renal-gingival syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "ers", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "absent enamel, nephrocalcinosis and apparently normal calcium metabolism", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta and nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta hypoplastic type, IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta nephrocalcinosis", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "amelogenesis imperfecta, type IG", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "enamel renal syndrome", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalised enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MONDO:0008771", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008771", "name": "generalized enamel hypoplasia and renal dysfunction", "description": "" }, { "id": "MIM:204690", "resource": "MIM", "url": "https://www.omim.org/entry/204690", "name": "Amelogenesis imperfecta 1G", "description": "Amelogenesis imperfecta 1G" } ], "unlinked_id_list": [], "evidence": [ { "id": "204690", "database": "MIM", "url": "https://www.omim.org/entry/204690" }, { "id": "0110066", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0110066" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q96MK3-1.388.388", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q96MK3-1.400.400", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TVKQIYPYNNSQRLLNVIDM", "down_seq": "IFDFLIGNMDRHHYEMFTKF", "snv": [ { "evidence": [ { "id": "Q96MK3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3" } ], "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": "17", "chr_pos": "68540870", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A400", "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": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q96MK3-1.388.388", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q96MK3-1.390.390", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.433.433", "start_pos": 433, "end_pos": 433, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2086212724", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2086212724", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2086212724", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2086212724#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HYEMFTKFGDDGFLIHLDNA", "down_seq": "GFGRHSHDEISILSPLSQCC", "snv": [ { "evidence": [ { "id": "rs2086212724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2086212724" }, { "id": "rs2086212724", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2086212724#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAR->NAS).", "chr_id": "17", "chr_pos": "68539887", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R433", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96MK3-1.540.540", "start_pos": 540, "end_pos": 540, "uniprot_canonical_ac": "Q96MK3-1", "length": 541, "uniprot_id": "FA20A_HUMAN", "protein_name": "Pseudokinase FAM20A", "refseq_ac": "NP_001230675", "refseq_name": "pseudokinase FAM20A isoform b", "gene_name": "FAM20A", "gene_names_uniprotkb": "FAM20A; PRO34279", "gene_names_refseq": "AI1G; AIGFS; FAM20A; FP2747", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96MK3", "url": "https://www.uniprot.org/uniprotkb/Q96MK3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96MK3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SVIVDGPVEQLAPDSGQANL", "down_seq": "", "snv": [ { "evidence": [ { "id": "Q96MK3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96MK3" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLI).", "chr_id": "17", "chr_pos": "68537484", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T540", "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": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "258", "end_pos": "258" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "70", "end_pos": "70" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q96MK3-1.538.538", "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": "P05019-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Insulin-like growth factor (IGF) signaling requires alphavbeta3-IGF1-IGF type 1 receptor (IGF1R) ternary complex formation in anchorage independence, and the complex formation does not require IGF1R and Src activation.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Fujita M, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "23243309", "url": "https://glygen.org/publication/PubMed/23243309" } ] }, { "title": "An integrin binding-defective mutant of insulin-like growth factor-1 (R36E/R37E IGF1) acts as a dominant-negative antagonist of the IGF1 receptor (IGF1R) and suppresses tumorigenesis but still binds to IGF1R.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Fujita M, Ieguchi K, Cedano-Prieto DM, Fong A, Wilkerson C, Chen JQ, Wu M, Lo SH, Cheung AT, Wilson MD, Cardiff RD, Borowsky AD, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "23696648", "url": "https://glygen.org/publication/PubMed/23696648" } ] }, { "title": "The direct binding of insulin-like growth factor-1 (IGF-1) to integrin alphavbeta3 is involved in IGF-1 signaling.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Saegusa J, Yamaji S, Ieguchi K, Wu CY, Lam KS, Liu FT, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "19578119", "url": "https://glygen.org/publication/PubMed/19578119" } ] }, { "title": "Cross-talk between integrin alpha6beta4 and insulin-like growth factor-1 receptor (IGF1R) through direct alpha6beta4 binding to IGF1 and subsequent alpha6beta4-IGF1-IGF1R ternary complex formation in anchorage-independent conditions.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Fujita M, Ieguchi K, Davari P, Yamaji S, Taniguchi Y, Sekiguchi K, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "22351760", "url": "https://glygen.org/publication/PubMed/22351760" } ] } ], "crossref": [ { "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23243309", "url": "https://glygen.org/publication/PubMed/23243309", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23696648", "url": "https://glygen.org/publication/PubMed/23696648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19578119", "url": "https://glygen.org/publication/PubMed/19578119", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22351760", "url": "https://glygen.org/publication/PubMed/22351760", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FVCGDRGFYFNKPTGYGSSS", "down_seq": "RAPQTGIVDECCFRSCDLRR", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "E", "comment": "Dominant-negative mutant, no effect on IGFR1-binding, defective in integrin-binding and the formation of ternary complex with integrins and IGFR1, defective in inducing IGF1 signaling and cell proliferation, and suppresses activation of IGF1R by insulin and tumorigenesis in vivo; when associated with E-85.", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" }, { "database": "PubMed", "id": "23243309", "url": "https://glygen.org/publication/PubMed/23243309" }, { "database": "PubMed", "id": "23696648", "url": "https://glygen.org/publication/PubMed/23696648" }, { "database": "PubMed", "id": "19578119", "url": "https://glygen.org/publication/PubMed/19578119" }, { "database": "PubMed", "id": "22351760", "url": "https://glygen.org/publication/PubMed/22351760" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P05019-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P05019-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P05019-1.98.98", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05019-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Insulin-like growth factor (IGF) signaling requires alphavbeta3-IGF1-IGF type 1 receptor (IGF1R) ternary complex formation in anchorage independence, and the complex formation does not require IGF1R and Src activation.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Fujita M, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "23243309", "url": "https://glygen.org/publication/PubMed/23243309" } ] }, { "title": "An integrin binding-defective mutant of insulin-like growth factor-1 (R36E/R37E IGF1) acts as a dominant-negative antagonist of the IGF1 receptor (IGF1R) and suppresses tumorigenesis but still binds to IGF1R.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Fujita M, Ieguchi K, Cedano-Prieto DM, Fong A, Wilkerson C, Chen JQ, Wu M, Lo SH, Cheung AT, Wilson MD, Cardiff RD, Borowsky AD, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "23696648", "url": "https://glygen.org/publication/PubMed/23696648" } ] }, { "title": "The direct binding of insulin-like growth factor-1 (IGF-1) to integrin alphavbeta3 is involved in IGF-1 signaling.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Saegusa J, Yamaji S, Ieguchi K, Wu CY, Lam KS, Liu FT, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "19578119", "url": "https://glygen.org/publication/PubMed/19578119" } ] }, { "title": "Cross-talk between integrin alpha6beta4 and insulin-like growth factor-1 receptor (IGF1R) through direct alpha6beta4 binding to IGF1 and subsequent alpha6beta4-IGF1-IGF1R ternary complex formation in anchorage-independent conditions.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Fujita M, Ieguchi K, Davari P, Yamaji S, Taniguchi Y, Sekiguchi K, Takada YK, Takada Y", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "reference": [ { "type": "PubMed", "id": "22351760", "url": "https://glygen.org/publication/PubMed/22351760" } ] } ], "crossref": [ { "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23243309", "url": "https://glygen.org/publication/PubMed/23243309", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23696648", "url": "https://glygen.org/publication/PubMed/23696648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19578119", "url": "https://glygen.org/publication/PubMed/19578119", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22351760", "url": "https://glygen.org/publication/PubMed/22351760", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VCGDRGFYFNKPTGYGSSSR", "down_seq": "APQTGIVDECCFRSCDLRRL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "E", "comment": "Dominant-negative mutant, no effect on IGFR1-binding, defective in integrin-binding and the formation of ternary complex with integrins and IGFR1, defective in inducing IGF1 signaling and cell proliferation, and suppresses activation of IGF1R by insulin and tumorigenesis in vivo; when associated with E-84.", "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" }, { "database": "PubMed", "id": "23243309", "url": "https://glygen.org/publication/PubMed/23243309" }, { "database": "PubMed", "id": "23696648", "url": "https://glygen.org/publication/PubMed/23696648" }, { "database": "PubMed", "id": "19578119", "url": "https://glygen.org/publication/PubMed/19578119" }, { "database": "PubMed", "id": "22351760", "url": "https://glygen.org/publication/PubMed/22351760" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P05019-1.84.84", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P05019-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P05019-1.98.98", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05019-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GIVDECCFRSCDLRRLEMYC", "down_seq": "PLKPAKSARSVRAQRHTDMP", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "102419583", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A110", "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": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P05019-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P05019-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P05019-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P05019-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P05019-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P05019-1.128.128", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SCDLRRLEMYCAPLKPAKSA", "down_seq": "SVRAQRHTDMPKTQKYQPPS", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "102419556", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R119", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P05019-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P05019-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P05019-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P05019-1.128.128", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LRRLEMYCAPLKPAKSARSV", "down_seq": "AQRHTDMPKTQKYQPPSTNK", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "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": "12", "chr_pos": "102419546", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R122", "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": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P05019-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P05019-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P05019-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P05019-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05019-1.142.142", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LEMYCAPLKPAKSARSVRAQ", "down_seq": "HTDMPKTQKYQPPSTNKNTK", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "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 (3).", "chr_id": "12", "chr_pos": "102419538", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R125", "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: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": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P05019-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P05019-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P05019-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P05019-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P05019-1.142.142", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YCAPLKPAKSARSVRAQRHT", "down_seq": "MPKTQKYQPPSTNKNTKSQR", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "102419529", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D128", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P05019-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P05019-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P05019-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P05019-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P05019-1.142.142", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RAQRHTDMPKTQKYQPPSTN", "down_seq": "NTKSQRRKGWPKTHPGGEQK", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "102417980", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K142", "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: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": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05019-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P05019-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P05019-1.128.128", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EQKEGTEASLQIRGKKKEQR", "down_seq": "EIGSRNAECRGKKGK", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "10", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient count (10/3601).", "chr_id": "12", "chr_pos": "102417866", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "R180", "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": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MGKISSLPTQLFKCCFCD", "down_seq": "LKVKMHTMSSSHLFYLALCL", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "102480325", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "F19", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P05019-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P05019-1.36.36", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05019-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLFKCCFCDFLKVKMHTMSS", "down_seq": "HLFYLALCLLTFTSSATAGP", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "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 (3).", "chr_id": "12", "chr_pos": "102475774", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S30", "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:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P05019-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P05019-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P05019-1.47.47", "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": "P05019-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FCDFLKVKMHTMSSSHLFYL", "down_seq": "LCLLTFTSSATAGPETLCGA", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "102475756", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A36", "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: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": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P05019-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P05019-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P05019-1.47.47", "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": "P05019-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "YFNKPTGYGSSSRRAPQTGI", "down_seq": "DECCFRSCDLRRLEMYCAPL", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "3", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "102419637", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V92", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID: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": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P05019-1.84.84", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P05019-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P05019-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P05019-1.110.110", "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": "P05019-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05019", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GYGSSSRRAPQTGIVDECCF", "down_seq": "SCDLRRLEMYCAPLKPAKSA", "snv": [ { "evidence": [ { "id": "P05019", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05019" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "102419618", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R98", "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: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": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P05019-1.84.84", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P05019-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P05019-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P05019-1.110.110", "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": "P05019-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P05019-1", "length": 195, "uniprot_id": "IGF1_HUMAN", "protein_name": "Insulin-like growth factor 1", "refseq_ac": "NP_000609", "refseq_name": "insulin-like growth factor 1 isoform 4 preproprotein", "gene_name": "IGF1", "gene_names_uniprotkb": "IGF1; IBP1; IGF-1", "gene_names_refseq": "IGF-I; IGF1; IGFI; IGF; MGF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05019", "url": "https://www.uniprot.org/uniprotkb/P05019" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Suppressive effect of membrane-permeable peptides derived from autophosphorylation sites of the IGF-1 receptor on breast cancer cells.", "journal": "European journal of pharmacology", "date": "2015", "authors": "Kuroda Y, Kato-Kogoe N, Tasaki E, Yuasa-Sunagawa M, Yamanegi K, Nakasho K, Nakase I, Futaki S, Tohyama Y, Hirose M", "evidence": [ { "database": "iPTMnet", "id": "P05019", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05019" } ], "reference": [ { "type": "PubMed", "id": "26276395", "url": "https://glygen.org/publication/PubMed/26276395" } ] } ], "crossref": [ { "id": "P05019", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05019", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "26276395", "url": "https://glygen.org/publication/PubMed/26276395", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSSSHLFYLALCLLTFTSSA", "down_seq": "AGPETLCGAELVDALQFVCG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05019", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05019" }, { "database": "PubMed", "id": "26276395", "url": "https://glygen.org/publication/PubMed/26276395" } ], "site_lbl": "Thr47" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P05019-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P05019-1.36.36", "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": "P35680-1.1.32", "start_pos": 1, "end_pos": 32, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mutations in PCBD1 cause hypomagnesemia and renal magnesium wasting.", "journal": "Journal of the American Society of Nephrology : JASN", "date": "2014", "authors": "Ferre S, de Baaij JH, Ferreira P, Germann R, de Klerk JB, Lavrijsen M, van Zeeland F, Venselaar H, Kluijtmans LA, Hoenderop JG, Bindels RJ", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "reference": [ { "type": "PubMed", "id": "24204001", "url": "https://glygen.org/publication/PubMed/24204001" } ] } ], "crossref": [ { "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24204001", "url": "https://glygen.org/publication/PubMed/24204001", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "MVSKLTSLQQELLSALLSSGVTKEVLVQALEE", "start_aa": "M", "up_seq": "", "down_seq": "LLPSPNFGVKLETLPLSPGS", "mutagenesis": [ { "sequence_org": "MVSKLTSLQQELLSALLSSGVTKEVLVQALEE", "sequence_mut": "", "comment": "Loss of interaction with PCBD1. Loss of PCBD1 recruitment to the nucleus.", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" }, { "database": "PubMed", "id": "24204001", "url": "https://glygen.org/publication/PubMed/24204001" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "P35680-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P35680-1.52.52", "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": "P35680-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mutations in PCBD1 cause hypomagnesemia and renal magnesium wasting.", "journal": "Journal of the American Society of Nephrology : JASN", "date": "2014", "authors": "Ferre S, de Baaij JH, Ferreira P, Germann R, de Klerk JB, Lavrijsen M, van Zeeland F, Venselaar H, Kluijtmans LA, Hoenderop JG, Bindels RJ", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "reference": [ { "type": "PubMed", "id": "24204001", "url": "https://glygen.org/publication/PubMed/24204001" } ] } ], "crossref": [ { "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24204001", "url": "https://glygen.org/publication/PubMed/24204001", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "RNRFKWGPASQQILYQAYDR", "down_seq": "KNPSKEEREALVEECNRAEC", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "P", "comment": "No impact on interaction with PCBD1. Reduced PCBD1 recruitment to the nucleus. Reduced coactivation by PCBD1.", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" }, { "database": "PubMed", "id": "24204001", "url": "https://glygen.org/publication/PubMed/24204001" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P35680-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P35680-1.241.241", "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": "P35680-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GTPMKTQKRAALYTWYVRKQ", "down_seq": "EILRQFNQTVQSSGNMTDKS", "snv": [ { "evidence": [ { "id": "P35680", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680" } ], "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": "17", "chr_pos": "37739454", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R177", "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": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P35680-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QSHGPGQSDDACSEPTNKKM", "down_seq": "RNRFKWGPASQQILYQAYDR", "snv": [ { "evidence": [ { "id": "P35680", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "37733672", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R232", "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:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P35680-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P35680-1.241.241", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P35680-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GPGQSDDACSEPTNKKMRRN", "down_seq": "FKWGPASQQILYQAYDRQKN", "snv": [ { "evidence": [ { "id": "P35680", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680" } ], "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": "17", "chr_pos": "37733663", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R235", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P35680-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P35680-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P35680-1.253.253", "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": "P35680-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DACSEPTNKKMRRNRFKWGP", "down_seq": "SQQILYQAYDRQKNPSKEER", "snv": [ { "evidence": [ { "id": "P35680", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "37733645", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A241", "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": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P35680-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P35680-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P35680-1.253.253", "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": "P35680-1.285.285", "start_pos": 285, "end_pos": 285, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VEECNRAECLQRGVSPSKAH", "down_seq": "LGSNLVTEVRVYNWFANRRK", "snv": [ { "evidence": [ { "id": "P35680", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680" } ], "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": "17", "chr_pos": "37731787", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G285", "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": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P35680-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P35680-1.303.303", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P35680-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QRGVSPSKAHGLGSNLVTEV", "down_seq": "VYNWFANRRKEEAFRQKLAM", "snv": [ { "evidence": [ { "id": "P35680", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "37731757", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R295", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P35680-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P35680-1.303.303", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P35680-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AHGLGSNLVTEVRVYNWFAN", "down_seq": "RKEEAFRQKLAMDAYSSNQT", "snv": [ { "evidence": [ { "id": "P35680", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P35680" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "37731732", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R303", "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: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": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P35680-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P35680-1.295.295", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P35680-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALEELLPSPNFGVKLETLPL", "down_seq": "PGSGAEPDTKPVFHTLTNGH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "site_lbl": "Ser49" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P35680-1.1.32", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P35680-1.52.52", "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": "P35680-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELLPSPNFGVKLETLPLSPG", "down_seq": "GAEPDTKPVFHTLTNGHAKG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "site_lbl": "Ser52" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P35680-1.1.32", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P35680-1.49.49", "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": "P35680-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPDTKPVFHTLTNGHAKGRL", "down_seq": "GDEGSEDGDDYDTPPILKEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "site_lbl": "Ser75" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P35680-1.80.80", "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": "P35680-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P35680-1", "length": 557, "uniprot_id": "HNF1B_HUMAN", "protein_name": "Hepatocyte nuclear factor 1-beta", "refseq_ac": "NP_000449", "refseq_name": "hepatocyte nuclear factor 1-beta isoform 1", "gene_name": "HNF1B", "gene_names_uniprotkb": "HNF1B; TCF2", "gene_names_refseq": "ADTKD3; FJHN; HNF-1-beta; HNF-1B; HNF1B; HNF1beta; HNF2; HPC11; LF-B3; LFB3; MODY5; RCAD; T2D; TCF-2; TCF2; VHNF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PVFHTLTNGHAKGRLSGDEG", "down_seq": "EDGDDYDTPPILKELQALNT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P35680", "url": "https://www.uniprot.org/uniprotkb/P35680" } ], "site_lbl": "Ser80" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1", "end_pos": "32" }, { "start_pos": "253", "end_pos": "253" } ] }, { "type": "snv", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "303", "end_pos": "303" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "49", "end_pos": "49" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "80", "end_pos": "80" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P35680-1.75.75", "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": "Q3MIT2-1.170.183", "start_pos": 170, "end_pos": 183, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "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": "QSLSLGRDDIVQLK", "start_aa": "Q", "up_seq": "PQLSVREHAAWLLVKQEMGK", "down_seq": "EAYKWITHPLFSEELGVPID", "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": "QSLSLGRDDIVQLK", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Gln", "end_aa": "Lys", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q3MIT2-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q3MIT2-1.171.171", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q3MIT2-1.173.173", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3MIT2-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.", "journal": "The EMBO journal", "date": "2013", "authors": "Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533" } ] }, { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "journal": "EMBO J", "date": "2013", "authors": "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs1205865209", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205865209", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1205865209", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1205865209#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1205865209", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205865209", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLSVREHAAWLLVKQEMGKQ", "down_seq": "LSLGRDDIVQLKEAYKWITH", "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": "Ser171", "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": "rs1205865209", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205865209" }, { "id": "rs1205865209", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1205865209#frequency_tab" }, { "id": "rs1205865209", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205865209" } ], "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": "60967604", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S171", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q3MIT2-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q3MIT2-1.170.183", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q3MIT2-1.173.173", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3MIT2-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.", "journal": "The EMBO journal", "date": "2013", "authors": "Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533" } ] }, { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "journal": "EMBO J", "date": "2013", "authors": "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs555560889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555560889", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs555560889", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555560889", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs555560889", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555560889#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs555560889", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555560889", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVREHAAWLLVKQEMGKQSL", "down_seq": "LGRDDIVQLKEAYKWITHPL", "glycosylation": [ { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser173", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs555560889", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555560889" }, { "id": "rs555560889", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555560889" }, { "id": "rs555560889", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555560889#frequency_tab" }, { "id": "rs555560889", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555560889" } ], "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": "2", "chr_pos": "60967599", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S173", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q3MIT2-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q3MIT2-1.170.183", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q3MIT2-1.171.171", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3MIT2-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation.", "journal": "Nature chemical biology", "date": "2020", "authors": "Song J, Zhuang Y, Zhu C, Meng H, Lu B, Xie B, Peng J, Li M, Yi C", "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" }, { "database": "RefSeq", "id": "NP_001309052", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001309052" } ], "reference": [ { "type": "PubMed", "id": "31819270", "url": "https://glygen.org/publication/PubMed/31819270" } ] }, { "title": "The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue.", "journal": "RNA (New York, N.Y.)", "date": "2019", "authors": "Deogharia M, Mukhopadhyay S, Joardar A, Gupta R", "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "reference": [ { "type": "PubMed", "id": "30530625", "url": "https://glygen.org/publication/PubMed/30530625" } ] } ], "crossref": [ { "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31819270", "url": "https://glygen.org/publication/PubMed/31819270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30530625", "url": "https://glygen.org/publication/PubMed/30530625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DHLLAVFKAESFNFSSSGRE", "down_seq": "VDVRTLGNGRPFAIELVNPH", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolished tRNA pseudouridine synthase without affecting ability to promote miRNA processing.", "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" }, { "database": "PubMed", "id": "31819270", "url": "https://glygen.org/publication/PubMed/31819270" }, { "database": "PubMed", "id": "30530625", "url": "https://glygen.org/publication/PubMed/30530625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "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": "Q3MIT2-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs372498476", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372498476", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372498476", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372498476", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372498476", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372498476#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372498476", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372498476", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs372498476", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs372498476", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NLSQNGEGRISVSHVGSTAS", "down_seq": "NSNLNVCNVCLGILQEFCEK", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" }, { "id": "rs372498476", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372498476" }, { "id": "rs372498476", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372498476" }, { "id": "rs372498476", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372498476#frequency_tab" }, { "id": "rs372498476", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372498476" }, { "id": "rs372498476", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs372498476" } ], "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 (KNS->NNS).", "chr_id": "2", "chr_pos": "61008836", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K102", "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": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q3MIT2-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q3MIT2-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q3MIT2-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q3MIT2-1.118.118", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1679409731", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1679409731", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1679409731", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1679409731#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1679409731", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1679409731", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QNGEGRISVSHVGSTASKNS", "down_seq": "LNVCNVCLGILQEFCEKDFI", "snv": [ { "evidence": [ { "id": "rs1679409731", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1679409731" }, { "id": "rs1679409731", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1679409731#frequency_tab" }, { "id": "rs1679409731", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1679409731" } ], "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": "2", "chr_pos": "61008828", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N105", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q3MIT2-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q3MIT2-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q3MIT2-1.118.118", "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": "Q3MIT2-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1299308676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299308676", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1299308676", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1299308676#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1299308676", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299308676", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GEGRISVSHVGSTASKNSNL", "down_seq": "VCNVCLGILQEFCEKDFIKK", "snv": [ { "evidence": [ { "id": "rs1299308676", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299308676" }, { "id": "rs1299308676", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1299308676#frequency_tab" }, { "id": "rs1299308676", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299308676" } ], "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 (NLN->NLS).", "chr_id": "2", "chr_pos": "61008822", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N107", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q3MIT2-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q3MIT2-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q3MIT2-1.118.118", "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": "Q3MIT2-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "STASKNSNLNVCNVCLGILQ", "down_seq": "FCEKDFIKKVCQKVEASGFE", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "61008790", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E118", "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": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q3MIT2-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q3MIT2-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q3MIT2-1.107.107", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PPQLSVREHAAWLLVKQEMG", "down_seq": "QSLSLGRDDIVQLKEAYKWI", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" } ], "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 (KQS->NQS).", "chr_id": "2", "chr_pos": "60967610", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K169", "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": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q3MIT2-1.170.183", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q3MIT2-1.171.171", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q3MIT2-1.173.173", "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": "Q3MIT2-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1679622707", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1679622707", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1679622707", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1679622707", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MFPLTEENKHVAQLLLNT", "down_seq": "TCPRCIFRFCGVDFHAPYKL", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTG->NTC).", "chr_id": "2", "chr_pos": "61011836", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G19", "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": "rs1679622707", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1679622707" }, { "id": "rs1679622707", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1679622707" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTG->NTS).", "chr_id": "2", "chr_pos": "61011836", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G19", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q3MIT2-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1676250405", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1676250405", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1676250405", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1676250405", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VEDCHFLAAICPDCFKPAKN", "down_seq": "QSVFTRMAVMKALNKIKEED", "snv": [ { "evidence": [ { "id": "rs1676250405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1676250405" }, { "id": "rs1676250405", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1676250405" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KQS->NQS).", "chr_id": "2", "chr_pos": "60965061", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K240", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs777350014", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777350014", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777350014", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777350014", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777350014", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777350014", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ALNKIKEEDFLKQFPCPPNS", "down_seq": "KAVCAVLEIECAHGAVFVAG", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" }, { "id": "rs777350014", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777350014" }, { "id": "rs777350014", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777350014" }, { "id": "rs777350014", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777350014" } ], "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 (NSP->NSS).", "chr_id": "2", "chr_pos": "60961523", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P272", "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": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ECAHGAVFVAGRYNKYSRNL", "down_seq": "QTPWIIDGERKLESSVEELI", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" } ], "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 (NLP->NLS).", "chr_id": "2", "chr_pos": "60960488", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P302", "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": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766465948", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766465948", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766465948", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766465948", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766465948", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766465948", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SALIWTNKAIQKKDIEFLND", "down_seq": "KDLKIDQKTPLRVLHRRPLA", "snv": [ { "evidence": [ { "id": "rs766465948", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766465948" }, { "id": "rs766465948", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766465948" }, { "id": "rs766465948", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766465948" } ], "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": "2", "chr_pos": "60953001", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I435", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q3MIT2-1.437.437", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q3MIT2-1.447.447", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.437.437", "start_pos": 437, "end_pos": 437, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LIWTNKAIQKKDIEFLNDIK", "down_seq": "LKIDQKTPLRVLHRRPLAVR", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" } ], "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": "2", "chr_pos": "60948185", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D437", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q3MIT2-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q3MIT2-1.447.447", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.447.447", "start_pos": 447, "end_pos": 447, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KDIEFLNDIKDLKIDQKTPL", "down_seq": "VLHRRPLAVRARVIHFMETQ", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" } ], "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": "2", "chr_pos": "60948154", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R447", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q3MIT2-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q3MIT2-1.437.437", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3MIT2-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3MIT2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LETEKDELILEVMNPPPKKI", "down_seq": "LQELEDSIDNLSQNGEGRIS", "snv": [ { "evidence": [ { "id": "Q3MIT2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3MIT2" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "61008928", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R72", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q3MIT2-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q3MIT2-1.84.84", "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": "Q3MIT2-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "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": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" }, { "database": "iPTMnet", "id": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] } ], "crossref": [ { "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LILEVMNPPPKKIRLQELED", "down_seq": "IDNLSQNGEGRISVSHVGST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "iPTMnet", "id": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2" } ], "site_lbl": "Ser79" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q3MIT2-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q3MIT2-1.84.84", "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": "Q3MIT2-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "Q3MIT2-1", "length": 529, "uniprot_id": "PUS10_HUMAN", "protein_name": "tRNA pseudouridine synthase Pus10", "refseq_ac": "NP_001309052", "refseq_name": "tRNA pseudouridine synthase Pus10 isoform 1", "gene_name": "PUS10", "gene_names_uniprotkb": "PUS10; CCDC139; DOBI", "gene_names_refseq": "CCDC139; DOBI; Hup10; PUS10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" } ], "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": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" }, { "database": "iPTMnet", "id": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science (New York, N.Y.)", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" }, { "database": "iPTMnet", "id": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2" } ], "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": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] } ], "crossref": [ { "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MNPPPKKIRLQELEDSIDNL", "down_seq": "QNGEGRISVSHVGSTASKNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q3MIT2", "url": "https://www.uniprot.org/uniprotkb/Q3MIT2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "iPTMnet", "id": "Q3MIT2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q3MIT2" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ], "site_lbl": "Ser84" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "170", "end_pos": "183" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "344", "end_pos": "344" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "79", "end_pos": "79" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q3MIT2-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q3MIT2-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q3MIT2-1.102.102", "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": "Q96IP4-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "Q96IP4-1", "length": 442, "uniprot_id": "TET5A_HUMAN", "protein_name": "Terminal nucleotidyltransferase 5A", "refseq_ac": "NP_060103", "refseq_name": "terminal nucleotidyltransferase 5A", "gene_name": "TENT5A", "gene_names_uniprotkb": "TENT5A; C6orf37; FAM46A; XTP11", "gene_names_refseq": "C6orf37; FAM46A; OI18; TENT5A; XTP11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cytoplasmic polyadenylation by TENT5A is required for proper bone formation.", "journal": "Cell reports", "date": "2021", "authors": "Gewartowska O, Aranaz-Novaliches G, Krawczyk PS, Mroczek S, Kusio-Kobialka M, Tarkowski B, Spoutil F, Benada O, Kofronova O, Szwedziak P, Cysewski D, Gruchota J, Szpila M, Chlebowski A, Sedlacek R, Prochazka J, Dziembowski A", "evidence": [ { "database": "UniProtKB", "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4" } ], "reference": [ { "type": "PubMed", "id": "33882302", "url": "https://glygen.org/publication/PubMed/33882302" } ] } ], "crossref": [ { "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33882302", "url": "https://glygen.org/publication/PubMed/33882302", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RLNGSAASHVLHQDSGLGYK", "down_seq": "LDLIFCADLRGEGEFQTVKD", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Does not elongate poly(A) tail; when associated with N-141.", "evidence": [ { "database": "UniProtKB", "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4" }, { "database": "PubMed", "id": "33882302", "url": "https://glygen.org/publication/PubMed/33882302" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q96IP4-1.141.141", "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": "Q96IP4-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "Q96IP4-1", "length": 442, "uniprot_id": "TET5A_HUMAN", "protein_name": "Terminal nucleotidyltransferase 5A", "refseq_ac": "NP_060103", "refseq_name": "terminal nucleotidyltransferase 5A", "gene_name": "TENT5A", "gene_names_uniprotkb": "TENT5A; C6orf37; FAM46A; XTP11", "gene_names_refseq": "C6orf37; FAM46A; OI18; TENT5A; XTP11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cytoplasmic polyadenylation by TENT5A is required for proper bone formation.", "journal": "Cell reports", "date": "2021", "authors": "Gewartowska O, Aranaz-Novaliches G, Krawczyk PS, Mroczek S, Kusio-Kobialka M, Tarkowski B, Spoutil F, Benada O, Kofronova O, Szwedziak P, Cysewski D, Gruchota J, Szpila M, Chlebowski A, Sedlacek R, Prochazka J, Dziembowski A", "evidence": [ { "database": "UniProtKB", "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4" } ], "reference": [ { "type": "PubMed", "id": "33882302", "url": "https://glygen.org/publication/PubMed/33882302" } ] } ], "crossref": [ { "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33882302", "url": "https://glygen.org/publication/PubMed/33882302", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NGSAASHVLHQDSGLGYKDL", "down_seq": "LIFCADLRGEGEFQTVKDVV", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Does not elongate poly(A) tail; when associated with N-139.", "evidence": [ { "database": "UniProtKB", "id": "Q96IP4", "url": "https://www.uniprot.org/uniprotkb/Q96IP4" }, { "database": "PubMed", "id": "33882302", "url": "https://glygen.org/publication/PubMed/33882302" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q96IP4-1.139.139", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BY41-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9BY41-1", "length": 377, "uniprot_id": "HDAC8_HUMAN", "protein_name": "Histone deacetylase 8", "refseq_ac": "NP_001159890", "refseq_name": "histone deacetylase 8 isoform 2", "gene_name": "HDAC8", "gene_names_uniprotkb": "HDAC8; CDA07; HDACL1", "gene_names_refseq": "CDA07; CDLS5; HD8; HDAC8; HDACL1; KDAC8; MRXS6; RPD3; WTS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "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": "Q9BY41", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BY41", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BY41", "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": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q9BY41", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BY41" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "142", "end_pos": "143" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "39", "end_pos": "39" } ] }, { "type": "snv", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "39", "end_pos": "39" } ] } ], "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": "Q9BY41-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "Q9BY41-1", "length": 377, "uniprot_id": "HDAC8_HUMAN", "protein_name": "Histone deacetylase 8", "refseq_ac": "NP_001159890", "refseq_name": "histone deacetylase 8 isoform 2", "gene_name": "HDAC8", "gene_names_uniprotkb": "HDAC8; CDA07; HDACL1", "gene_names_refseq": "CDA07; CDLS5; HD8; HDAC8; HDACL1; KDAC8; MRXS6; RPD3; WTS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.", "journal": "Biochemistry", "date": "2008", "authors": "Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282" } ] }, { "title": "Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex.", "journal": "EMBO reports", "date": "2007", "authors": "Vannini A, Volpari C, Gallinari P, Jones P, Mattu M, Carfi A, De Francesco R, Steinkuhler C, Di Marco S", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440" } ] } ], "crossref": [ { "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KVSQEGDDDHPDSIEYGLGY", "down_seq": "CPATEGIFDYAAAIGGATIT", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Complete loss of catalytical activity. Complete loss of catalytical activity; when associated with F-306.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282" }, { "database": "PubMed", "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440" } ] }, { "sequence_org": "D", "sequence_mut": "E", "comment": "Partial loss of catalytical activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282" }, { "database": "PubMed", "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440" } ] }, { "sequence_org": "D", "sequence_mut": "L", "comment": "Complete loss of catalytical activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282" }, { "database": "PubMed", "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440" } ] }, { "sequence_org": "D", "sequence_mut": "N", "comment": "Almost complete loss of catalytical activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282" }, { "database": "PubMed", "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "142", "end_pos": "143" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "39", "end_pos": "39" } ] }, { "type": "snv", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "39", "end_pos": "39" } ] } ], "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": "Q9BY41-1.142.143", "start_pos": 142, "end_pos": 143, "uniprot_canonical_ac": "Q9BY41-1", "length": 377, "uniprot_id": "HDAC8_HUMAN", "protein_name": "Histone deacetylase 8", "refseq_ac": "NP_001159890", "refseq_name": "histone deacetylase 8 isoform 2", "gene_name": "HDAC8", "gene_names_uniprotkb": "HDAC8; CDA07; HDACL1", "gene_names_refseq": "CDA07; CDLS5; HD8; HDAC8; HDACL1; KDAC8; MRXS6; RPD3; WTS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Cloning and characterization of a novel human histone deacetylase, HDAC8.", "journal": "The Biochemical journal", "date": "2000", "authors": "Buggy JJ, Sideris ML, Mak P, Lorimer DD, McIntosh B, Clark JM", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "Reactome", "id": "R-HSA-3214815", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3214815" } ], "reference": [ { "type": "PubMed", "id": "10926844", "url": "https://glygen.org/publication/PubMed/10926844" } ] } ], "crossref": [ { "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10926844", "url": "https://glygen.org/publication/PubMed/10926844", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "HH", "start_aa": "H", "up_seq": "AAQCLIDGMCKVAINWSGGW", "down_seq": "AKKDEASGFCYLNDAVLGIL", "mutagenesis": [ { "sequence_org": "HH", "sequence_mut": "AA", "comment": "Strongly reduces histone deacetylase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "10926844", "url": "https://glygen.org/publication/PubMed/10926844" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "142", "end_pos": "143" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "39", "end_pos": "39" } ] }, { "type": "snv", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "39", "end_pos": "39" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 0, "direction": "upstream", "id": "Q9BY41-1.143.143", "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": "Q9BY41-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "Q9BY41-1", "length": 377, "uniprot_id": "HDAC8_HUMAN", "protein_name": "Histone deacetylase 8", "refseq_ac": "NP_001159890", "refseq_name": "histone deacetylase 8 isoform 2", "gene_name": "HDAC8", "gene_names_uniprotkb": "HDAC8; CDA07; HDACL1", "gene_names_refseq": "CDA07; CDLS5; HD8; HDAC8; HDACL1; KDAC8; MRXS6; RPD3; WTS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.", "journal": "Biochemistry", "date": "2008", "authors": "Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282" } ] } ], "crossref": [ { "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "AQCLIDGMCKVAINWSGGWH", "down_seq": "AKKDEASGFCYLNDAVLGIL", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Loss of catalytic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "19053282", "url": "https://glygen.org/publication/PubMed/19053282" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "142", "end_pos": "143" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "39", "end_pos": "39" } ] }, { "type": "snv", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "39", "end_pos": "39" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 0, "direction": "downstream", "id": "Q9BY41-1.142.143", "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": "Q9BY41-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "Q9BY41-1", "length": 377, "uniprot_id": "HDAC8_HUMAN", "protein_name": "Histone deacetylase 8", "refseq_ac": "NP_001159890", "refseq_name": "histone deacetylase 8 isoform 2", "gene_name": "HDAC8", "gene_names_uniprotkb": "HDAC8; CDA07; HDACL1", "gene_names_refseq": "CDA07; CDLS5; HD8; HDAC8; HDACL1; KDAC8; MRXS6; RPD3; WTS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex.", "journal": "EMBO reports", "date": "2007", "authors": "Vannini A, Volpari C, Gallinari P, Jones P, Mattu M, Carfi A, De Francesco R, Steinkuhler C, Di Marco S", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440" } ] } ], "crossref": [ { "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KCLKYILQWQLATLILGGGG", "down_seq": "NLANTARCWTYLTGVILGKT", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Loss of catalytic activity. Complete loss of catalytic activity; when associated with A-101.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "17721440", "url": "https://glygen.org/publication/PubMed/17721440" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "142", "end_pos": "143" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "39", "end_pos": "39" } ] }, { "type": "snv", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "39", "end_pos": "39" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9BY41-1.311.311", "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": "Q9BY41-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "Q9BY41-1", "length": 377, "uniprot_id": "HDAC8_HUMAN", "protein_name": "Histone deacetylase 8", "refseq_ac": "NP_001159890", "refseq_name": "histone deacetylase 8 isoform 2", "gene_name": "HDAC8", "gene_names_uniprotkb": "HDAC8; CDA07; HDACL1", "gene_names_refseq": "CDA07; CDLS5; HD8; HDAC8; HDACL1; KDAC8; MRXS6; RPD3; WTS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Negative regulation of histone deacetylase 8 activity by cyclic AMP-dependent protein kinase A.", "journal": "Molecular and cellular biology", "date": "2004", "authors": "Lee H, Rezai-Zadeh N, Seto E", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "iPTMnet", "id": "Q9BY41-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BY41-1" } ], "reference": [ { "type": "PubMed", "id": "14701748", "url": "https://glygen.org/publication/PubMed/14701748" } ] }, { "title": "Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases.", "journal": "Structure (London, England : 1993)", "date": "2004", "authors": "Somoza JR, Skene RJ, Katz BA, Mol C, Ho JD, Jennings AJ, Luong C, Arvai A, Buggy JJ, Chi E, Tang J, Sang BC, Verner E, Wynands R, Leahy EM, Dougan DR, Snell G, Navre M, Knuth MW, Swanson RV, McRee DE, Tari LW", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "iPTMnet", "id": "Q9BY41", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "15242608", "url": "https://glygen.org/publication/PubMed/15242608" } ] }, { "title": "Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8.", "journal": "Journal of the American Chemical Society", "date": "2013", "authors": "Kunze MB, Wright DW, Werbeck ND, Kirkpatrick J, Coveney PV, Hansen DF", "evidence": [ { "database": "iPTMnet", "id": "Q9BY41", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "24171457", "url": "https://glygen.org/publication/PubMed/24171457" } ] }, { "title": "Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6.", "journal": "Cell communication and signaling : CCS", "date": "2018", "authors": "Vanaja GR, Ramulu HG, Kalle AM", "evidence": [ { "database": "iPTMnet", "id": "Q9BY41", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BY41" } ], "reference": [ { "type": "PubMed", "id": "29716651", "url": "https://glygen.org/publication/PubMed/29716651" } ] } ], "crossref": [ { "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "14701748", "url": "https://glygen.org/publication/PubMed/14701748", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BY41", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BY41", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15242608", "url": "https://glygen.org/publication/PubMed/15242608", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24171457", "url": "https://glygen.org/publication/PubMed/24171457", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29716651", "url": "https://glygen.org/publication/PubMed/29716651", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IYSPEYVSMCDSLAKIPKRA", "down_seq": "MVHSLIEAYALHKQMRIVKP", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Enhances the deacetylase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "14701748", "url": "https://glygen.org/publication/PubMed/14701748" } ] }, { "sequence_org": "S", "sequence_mut": "E", "comment": "Decreases the deacetylase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "14701748", "url": "https://glygen.org/publication/PubMed/14701748" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P17612-1", "kinase_gene_name": "PRKACA", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BY41", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BY41" }, { "database": "PubMed", "id": "14701748", "url": "https://glygen.org/publication/PubMed/14701748" } ], "site_lbl": "Ser39" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" }, { "database": "PubMed", "id": "15242608", "url": "https://glygen.org/publication/PubMed/15242608" }, { "database": "iPTMnet", "id": "Q9BY41", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BY41" }, { "database": "PubMed", "id": "14701748", "url": "https://glygen.org/publication/PubMed/14701748" }, { "database": "PubMed", "id": "24171457", "url": "https://glygen.org/publication/PubMed/24171457" }, { "database": "PubMed", "id": "29716651", "url": "https://glygen.org/publication/PubMed/29716651" } ], "site_lbl": "Ser39" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "142", "end_pos": "143" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "39", "end_pos": "39" } ] }, { "type": "snv", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "39", "end_pos": "39" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BY41-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "Q9BY41-1", "length": 377, "uniprot_id": "HDAC8_HUMAN", "protein_name": "Histone deacetylase 8", "refseq_ac": "NP_001159890", "refseq_name": "histone deacetylase 8 isoform 2", "gene_name": "HDAC8", "gene_names_uniprotkb": "HDAC8; CDA07; HDACL1", "gene_names_refseq": "CDA07; CDLS5; HD8; HDAC8; HDACL1; KDAC8; MRXS6; RPD3; WTS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BY41", "url": "https://www.uniprot.org/uniprotkb/Q9BY41" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BY41", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BY41", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ILQWQLATLILGGGGYNLAN", "down_seq": "ARCWTYLTGVILGKTLSSEI", "snv": [ { "evidence": [ { "id": "Q9BY41", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BY41" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "72462077", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T311", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID: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": "101", "end_pos": "101" }, { "start_pos": "142", "end_pos": "143" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "39", "end_pos": "39" } ] }, { "type": "snv", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "39", "end_pos": "39" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BY41-1.306.306", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14902-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P14902-1", "length": 403, "uniprot_id": "I23O1_HUMAN", "protein_name": "Indoleamine 2,3-dioxygenase 1", "refseq_ac": "NP_002155", "refseq_name": "indoleamine 2,3-dioxygenase 1", "gene_name": "IDO1", "gene_names_uniprotkb": "IDO1; IDO; INDO", "gene_names_refseq": "IDO-1; IDO1; IDO; INDO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14902", "url": "https://www.uniprot.org/uniprotkb/P14902" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14902", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KKKDPNKPLTYENMDVLFSF", "down_seq": "DGDCSKGFFLVSLLVEIAAA", "snv": [ { "evidence": [ { "id": "P14902", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "8", "frequency": "0.4", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "39922577", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R155", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "329", "end_pos": "329" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14902-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "P14902-1", "length": 403, "uniprot_id": "I23O1_HUMAN", "protein_name": "Indoleamine 2,3-dioxygenase 1", "refseq_ac": "NP_002155", "refseq_name": "indoleamine 2,3-dioxygenase 1", "gene_name": "IDO1", "gene_names_uniprotkb": "IDO1; IDO; INDO", "gene_names_refseq": "IDO-1; IDO1; IDO; INDO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14902", "url": "https://www.uniprot.org/uniprotkb/P14902" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14902", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQVFHQIHDHVNPKAFFSVL", "down_seq": "IYLSGWKGNPQLSDGLVYEG", "snv": [ { "evidence": [ { "id": "P14902", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "39924756", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R231", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "329", "end_pos": "329" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14902-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "P14902-1", "length": 403, "uniprot_id": "I23O1_HUMAN", "protein_name": "Indoleamine 2,3-dioxygenase 1", "refseq_ac": "NP_002155", "refseq_name": "indoleamine 2,3-dioxygenase 1", "gene_name": "IDO1", "gene_names_uniprotkb": "IDO1; IDO; INDO", "gene_names_refseq": "IDO-1; IDO1; IDO; INDO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14902", "url": "https://www.uniprot.org/uniprotkb/P14902" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14902", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "GHAAQFLQDMRRYMPPAHRN", "down_seq": "LCSLESNPSVREFVLSKGDA", "snv": [ { "evidence": [ { "id": "P14902", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "39927889", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "F306", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "329", "end_pos": "329" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14902-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "P14902-1", "length": 403, "uniprot_id": "I23O1_HUMAN", "protein_name": "Indoleamine 2,3-dioxygenase 1", "refseq_ac": "NP_002155", "refseq_name": "indoleamine 2,3-dioxygenase 1", "gene_name": "IDO1", "gene_names_uniprotkb": "IDO1; IDO; INDO", "gene_names_refseq": "IDO-1; IDO1; IDO; INDO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14902", "url": "https://www.uniprot.org/uniprotkb/P14902" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14902", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SLESNPSVREFVLSKGDAGL", "down_seq": "EAYDACVKALVSLRSYHLQI", "snv": [ { "evidence": [ { "id": "P14902", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14902" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "39927959", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R329", "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": "155", "end_pos": "155" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "329", "end_pos": "329" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.348.348", "start_pos": 348, "end_pos": 348, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VNAASGGVQNSGIVREAPAT", "down_seq": "IATVLPQPMTSAMGKGTVAV", "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": "Ser348", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q8NHV4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NHV4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHV4-1.329.329", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHV4-1.351.351", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHV4-1.358.358", "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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.351.351", "start_pos": 351, "end_pos": 351, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "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": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "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": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1301791155", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1301791155", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1301791155", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1301791155#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1301791155", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1301791155", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ASGGVQNSGIVREAPATSIA", "down_seq": "VLPQPMTSAMGKGTVAVQEK", "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": "Thr351", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q8NHV4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "Q8NHV4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ] } ], "snv": [ { "evidence": [ { "id": "rs1301791155", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1301791155" }, { "id": "rs1301791155", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1301791155#frequency_tab" }, { "id": "rs1301791155", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1301791155" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "12", "chr_pos": "96937327", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T351", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NHV4-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHV4-1.348.348", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHV4-1.358.358", "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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.358.358", "start_pos": 358, "end_pos": 358, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs200008061", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200008061", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200008061", "url": "https://www.ensembl.org/id/rs200008061", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SGIVREAPATSIATVLPQPM", "down_seq": "SAMGKGTVAVQEKAGLPRSI", "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": "Thr358", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q8NHV4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NHV4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ] } ], "snv": [ { "evidence": [ { "id": "rs200008061", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200008061" }, { "id": "rs200008061", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs200008061" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "12", "chr_pos": "96937348", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T358", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8NHV4-1.348.348", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHV4-1.351.351", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHV4-1.377.377", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Regulation of microtubule-based microtubule nucleation by mammalian polo-like kinase 1.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Johmura Y, Soung NK, Park JE, Yu LR, Zhou M, Bang JK, Kim BY, Veenstra TD, Erikson RL, Lee KS", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "21690413", "url": "https://glygen.org/publication/PubMed/21690413" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1050517522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1050517522", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1050517522", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1050517522#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1050517522", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1050517522", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs80238813", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs80238813", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs80238813", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs80238813", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs80238813", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs80238813", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs80238813", "url": "https://www.ncbi.nlm.nih.gov/snp/rs80238813#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs80238813", "url": "http://gnomad.broadinstitute.org/awesome?query=rs80238813", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21690413", "url": "https://glygen.org/publication/PubMed/21690413", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSVFPPRKNPVTSSTSVLHS", "down_seq": "PLNVFMGSPGKEENENRDLT", "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": "Ser460", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q8NHV4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NHV4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ] } ], "snv": [ { "evidence": [ { "id": "rs1050517522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1050517522" }, { "id": "rs1050517522", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1050517522#frequency_tab" }, { "id": "rs1050517522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1050517522" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "12", "chr_pos": "96943643", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S460", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs80238813", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs80238813" }, { "id": "rs80238813", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs80238813" }, { "id": "rs80238813", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs80238813" }, { "id": "rs80238813", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs80238813#frequency_tab" }, { "id": "rs80238813", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs80238813" }, { "id": "rs1050517522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1050517522" }, { "id": "rs1050517522", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1050517522#frequency_tab" }, { "id": "rs1050517522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1050517522" } ], "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": "12", "chr_pos": "96943645", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "S460", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "21690413", "url": "https://glygen.org/publication/PubMed/21690413" } ], "site_lbl": "Ser460" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8NHV4-1.468.468", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.493.493", "start_pos": 493, "end_pos": 493, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ENENRDLTAESKKIYMGKQE", "down_seq": "KDSFKQLAKLVTSGAESGNL", "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": "Ser493", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q8NHV4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NHV4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q8NHV4-1.506.506", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHV4", "url": "https://oglcnac.org/atlas/detail/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IYMGKQESKDSFKQLAKLVT", "down_seq": "GAESGNLNTSPSSNQTRNSE", "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": "Ser506", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q8NHV4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHV4" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8NHV4-1.493.493", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHV4-1.514.514", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHV4-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHV4-1.516.516", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHV4-1.518.518", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.514.514", "start_pos": 514, "end_pos": 514, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "rs1878015959", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1878015959", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1878015959", "url": "https://www.ensembl.org/id/rs1878015959", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KDSFKQLAKLVTSGAESGNL", "down_seq": "TSPSSNQTRNSEKFEKPENE", "glycosylation": [ { "glytoucan_ac": "G84349RE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DSFKQLAKLVTSGAESGNLNTSPSSNQTR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn514", "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": "rs1878015959", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1878015959" }, { "id": "rs1878015959", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1878015959" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->DTS).", "chr_id": "12", "chr_pos": "96944681", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N514", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NHV4-1.506.506", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHV4-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHV4-1.516.516", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHV4-1.518.518", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201464037", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201464037", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201464037", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201464037", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201464037", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201464037#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201464037", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201464037", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RVHRSLKDHKDQVTCVTYNW", "down_seq": "DCYIASGSLSGEIILHSVTT", "snv": [ { "evidence": [ { "id": "rs201464037", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201464037" }, { "id": "rs201464037", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201464037" }, { "id": "rs201464037", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201464037#frequency_tab" }, { "id": "rs201464037", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201464037" } ], "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 (NWN->NWS).", "chr_id": "12", "chr_pos": "96920025", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N130", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.147.147", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771770342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771770342", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771770342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771770342", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771770342", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771770342", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YNWNDCYIASGSLSGEIILH", "down_seq": "VTTNLSSTPFGHGSNQSVRH", "snv": [ { "evidence": [ { "id": "rs771770342", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771770342" }, { "id": "rs771770342", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771770342" }, { "id": "rs771770342", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771770342" } ], "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": "12", "chr_pos": "96920076", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S147", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.130.130", "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": "Q8NHV4-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1339264907", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1339264907", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1339264907", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1339264907", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSNQSVRHLKYSLFKKSLLG", "down_seq": "VSDNGIVTLWDVNSQSPYHN", "snv": [ { "evidence": [ { "id": "rs1339264907", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1339264907" }, { "id": "rs1339264907", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1339264907" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SVS->NVS).", "chr_id": "12", "chr_pos": "96935025", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S180", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs555575064", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555575064", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs555575064", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555575064", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs555575064", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555575064", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs555575064", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555575064#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs555575064", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555575064", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs555575064", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555575064", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MQENLRFASSGDDIKIW", "down_seq": "ASSMTLVDKFNPHTSPHGIS", "snv": [ { "evidence": [ { "id": "rs555575064", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555575064" }, { "id": "rs555575064", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555575064" }, { "id": "rs555575064", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555575064" }, { "id": "rs555575064", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555575064#frequency_tab" }, { "id": "rs555575064", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555575064" }, { "id": "rs555575064", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555575064" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DAS->NAS).", "chr_id": "12", "chr_pos": "96909811", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D18", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHV4-1.6.6", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1232880398", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1232880398", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1232880398", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1232880398#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1232880398", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1232880398", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SPVNELLFVTIGLDKRIILY", "down_seq": "TSSKKLVKTLVADTPLTAVD", "snv": [ { "evidence": [ { "id": "rs1232880398", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1232880398" }, { "id": "rs1232880398", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1232880398#frequency_tab" }, { "id": "rs1232880398", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1232880398" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DTS->NTS).", "chr_id": "12", "chr_pos": "96935189", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D235", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8NHV4-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHV4-1.238.238", "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": "Q8NHV4-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765077598", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765077598", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765077598", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765077598", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765077598", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765077598", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GSSRGKIYQYDLRMLKSPVK", "down_seq": "ISAHKTSVQCIAFQYSTVLT", "snv": [ { "evidence": [ { "id": "rs765077598", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765077598" }, { "id": "rs765077598", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765077598" }, { "id": "rs765077598", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765077598" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TIS->NIS).", "chr_id": "12", "chr_pos": "96936748", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T286", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q8NHV4-1.301.301", "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": "Q8NHV4-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1592913929", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1592913929", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1592913929", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1592913929", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KSPVKTISAHKTSVQCIAFQ", "down_seq": "STVLTKSSLNKGCSNKPTTV", "snv": [ { "evidence": [ { "id": "rs1592913929", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1592913929" }, { "id": "rs1592913929", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1592913929" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YST->NST).", "chr_id": "12", "chr_pos": "96936792", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHV4-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHV4-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHV4-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.318.318", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1254180942", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254180942", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1254180942", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254180942", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TSVQCIAFQYSTVLTKSSLN", "down_seq": "GCSNKPTTVNKRSVNVNAAS", "snv": [ { "evidence": [ { "id": "rs1254180942", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254180942" }, { "id": "rs1254180942", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254180942" } ], "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": "12", "chr_pos": "96937212", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K312", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NHV4-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHV4-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHV4-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHV4-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.329.329", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHV4-1.331.331", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHV4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SVQCIAFQYSTVLTKSSLNK", "down_seq": "CSNKPTTVNKRSVNVNAASG", "snv": [ { "evidence": [ { "id": "Q8NHV4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKG->NKC).", "chr_id": "12", "chr_pos": "96937213", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G313", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHV4-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHV4-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHV4-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHV4-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHV4-1.329.329", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHV4-1.331.331", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1388778028", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1388778028", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1388778028", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1388778028", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AFQYSTVLTKSSLNKGCSNK", "down_seq": "TTVNKRSVNVNAASGGVQNS", "snv": [ { "evidence": [ { "id": "rs1388778028", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1388778028" }, { "id": "rs1388778028", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1388778028" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKT).", "chr_id": "12", "chr_pos": "96937228", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P318", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHV4-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHV4-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHV4-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHV4-1.329.329", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHV4-1.331.331", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1274257056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1274257056", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1274257056", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1274257056#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1274257056", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1274257056", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SLNKGCSNKPTTVNKRSVNV", "down_seq": "AASGGVQNSGIVREAPATSI", "snv": [ { "evidence": [ { "id": "rs1274257056", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1274257056" }, { "id": "rs1274257056", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1274257056#frequency_tab" }, { "id": "rs1274257056", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1274257056" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVN->NVS).", "chr_id": "12", "chr_pos": "96937262", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N329", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHV4-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NHV4-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHV4-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHV4-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHV4-1.348.348", "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": "Q8NHV4-1.331.331", "start_pos": 331, "end_pos": 331, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs149842178", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149842178", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149842178", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149842178", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149842178", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149842178", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NKGCSNKPTTVNKRSVNVNA", "down_seq": "SGGVQNSGIVREAPATSIAT", "snv": [ { "evidence": [ { "id": "rs149842178", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149842178" }, { "id": "rs149842178", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149842178" }, { "id": "rs149842178", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149842178" } ], "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": "12", "chr_pos": "96937267", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A331", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHV4-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8NHV4-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8NHV4-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHV4-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHV4-1.329.329", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.348.348", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NHV4-1.351.351", "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": "Q8NHV4-1.394.394", "start_pos": 394, "end_pos": 394, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760875905", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760875905", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760875905", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760875905", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760875905", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760875905#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760875905", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760875905", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LPRSINTDTLSKETDSGKNQ", "down_seq": "FSSFDDTGKSSLGDMFSPIR", "snv": [ { "evidence": [ { "id": "rs760875905", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760875905" }, { "id": "rs760875905", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760875905" }, { "id": "rs760875905", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760875905#frequency_tab" }, { "id": "rs760875905", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760875905" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DFS->NFS).", "chr_id": "12", "chr_pos": "96940471", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D394", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.377.377", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8NHV4-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHV4-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHV4-1.405.405", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.411.411", "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": "Q8NHV4-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1177574943", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177574943", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1177574943", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177574943", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "FNPHTSPHGISSICWSSNNN", "down_seq": "LVTASSSGDKIVVSSCKCKP", "snv": [ { "evidence": [ { "id": "rs1177574943", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177574943" }, { "id": "rs1177574943", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177574943" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNF->NNC).", "chr_id": "12", "chr_pos": "96912729", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F48", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8NHV4-1.49.49", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1254563081", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254563081", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1254563081", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254563081", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NPHTSPHGISSICWSSNNNF", "down_seq": "VTASSSGDKIVVSSCKCKPV", "snv": [ { "evidence": [ { "id": "rs1254563081", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254563081" }, { "id": "rs1254563081", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254563081" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFL->NFS).", "chr_id": "12", "chr_pos": "96912732", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L49", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8NHV4-1.48.48", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.516.516", "start_pos": 516, "end_pos": 516, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "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": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] }, { "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": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] }, { "title": "Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages.", "journal": "Journal of proteome research", "date": "2009", "authors": "Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "rs1159072088", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159072088", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1159072088", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159072088#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1159072088", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1159072088", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SFKQLAKLVTSGAESGNLNT", "down_seq": "PSSNQTRNSEKFEKPENEIE", "snv": [ { "evidence": [ { "id": "rs1159072088", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159072088" }, { "id": "rs1159072088", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159072088#frequency_tab" }, { "id": "rs1159072088", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1159072088" } ], "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 (NTS->NTF).", "chr_id": "12", "chr_pos": "96944688", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S516", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser516" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8NHV4-1.506.506", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHV4-1.514.514", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHV4-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHV4-1.518.518", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHV4-1.535.535", "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": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.535.535", "start_pos": 535, "end_pos": 535, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758941625", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758941625", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758941625", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758941625", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758941625", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758941625", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TSPSSNQTRNSEKFEKPENE", "down_seq": "EAQLICEPPINGSSTPNPKI", "snv": [ { "evidence": [ { "id": "rs758941625", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758941625" }, { "id": "rs758941625", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758941625" }, { "id": "rs758941625", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758941625" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEI->NET).", "chr_id": "12", "chr_pos": "96944745", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I535", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NHV4-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8NHV4-1.516.516", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.518.518", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHV4-1.548.548", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHV4-1.550.550", "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": "Q8NHV4-1.548.548", "start_pos": 548, "end_pos": 548, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHV4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FEKPENEIEAQLICEPPING", "down_seq": "STPNPKIASSVTAGVASSLS", "snv": [ { "evidence": [ { "id": "Q8NHV4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "96944784", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S548", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8NHV4-1.535.535", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHV4-1.550.550", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHV4-1.557.557", "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": "Q8NHV4-1.583.583", "start_pos": 583, "end_pos": 583, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1443360681", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443360681", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443360681", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443360681", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VASSLSEKIADSIGNNRQNA", "down_seq": "LTSIQIRFIQNMIQETLDDF", "snv": [ { "evidence": [ { "id": "rs1443360681", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443360681" }, { "id": "rs1443360681", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443360681" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAP->NAS).", "chr_id": "12", "chr_pos": "96945785", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P583", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8NHV4-1.574.574", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHV4-1.590.590", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.590.590", "start_pos": 590, "end_pos": 590, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHV4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KIADSIGNNRQNAPLTSIQI", "down_seq": "FIQNMIQETLDDFREACHRD", "snv": [ { "evidence": [ { "id": "Q8NHV4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4" } ], "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": "12", "chr_pos": "96945806", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R590", "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": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NHV4-1.574.574", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHV4-1.583.583", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHV4-1.608.608", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.608.608", "start_pos": 608, "end_pos": 608, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHV4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "QIRFIQNMIQETLDDFREAC", "down_seq": "RDIVNLQVEMIKQFHMQLNE", "snv": [ { "evidence": [ { "id": "Q8NHV4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHV4" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "H", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "96951443", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "H608", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHV4-1.590.590", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q8NHV4-1.641.641", "start_pos": 641, "end_pos": 641, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1421495855", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421495855", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1421495855", "url": "https://www.ensembl.org/id/rs1421495855", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "QFHMQLNEMHSLLERYSVNE", "down_seq": "LVAEIERLREENKRLRAHF", "snv": [ { "evidence": [ { "id": "rs1421495855", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421495855" }, { "id": "rs1421495855", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1421495855" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEG->NES).", "chr_id": "12", "chr_pos": "96951991", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G641", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8NHV4-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHV4-1.655.655", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.655.655", "start_pos": 655, "end_pos": 655, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751393737", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751393737", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751393737", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751393737", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751393737", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751393737#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751393737", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751393737", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RYSVNEGLVAEIERLREENK", "down_seq": "LRAHF", "snv": [ { "evidence": [ { "id": "rs751393737", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751393737" }, { "id": "rs751393737", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751393737" }, { "id": "rs751393737", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751393737#frequency_tab" }, { "id": "rs751393737", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751393737" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKR->NKS).", "chr_id": "12", "chr_pos": "96952035", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R655", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHV4-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHV4-1.641.641", "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": "Q8NHV4-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765461360", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765461360", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765461360", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765461360", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765461360", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765461360#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765461360", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765461360", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MQENL", "down_seq": "FASSGDDIKIWDASSMTLVD", "snv": [ { "evidence": [ { "id": "rs765461360", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765461360" }, { "id": "rs765461360", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765461360" }, { "id": "rs765461360", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765461360#frequency_tab" }, { "id": "rs765461360", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765461360" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLR->NLT).", "chr_id": "12", "chr_pos": "96909776", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R6", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q8NHV4-1.18.18", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHV4-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "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": "VNELLFVTIGLDKRIILYDT", "down_seq": "SKKLVKTLVADTPLTAVDFM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser237" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8NHV4-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHV4-1.238.238", "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": "Q8NHV4-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "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": "NELLFVTIGLDKRIILYDTS", "down_seq": "KKLVKTLVADTPLTAVDFMP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser238" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8NHV4-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHV4-1.237.237", "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": "Q8NHV4-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "PLK4-phosphorylated NEDD1 facilitates cartwheel assembly and centriole biogenesis initiations.", "journal": "The Journal of cell biology", "date": "2021", "authors": "Chi W, Wang G, Xin G, Jiang Q, Zhang C", "evidence": [ { "database": "RefSeq", "id": "NP_001128647", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001128647" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "33351100", "url": "https://glygen.org/publication/PubMed/33351100" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33351100", "url": "https://glygen.org/publication/PubMed/33351100", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LTKSSLNKGCSNKPTTVNKR", "down_seq": "VNVNAASGGVQNSGIVREAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "33351100", "url": "https://glygen.org/publication/PubMed/33351100" } ], "site_lbl": "Ser325" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8NHV4-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8NHV4-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHV4-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHV4-1.329.329", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHV4-1.331.331", "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": "Q8NHV4-1.377.377", "start_pos": 377, "end_pos": 377, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Nek9 phosphorylation of NEDD1/GCP-WD contributes to Plk1 control of gamma-tubulin recruitment to the mitotic centrosome.", "journal": "Current biology : CB", "date": "2012", "authors": "Sdelci S, Schutz M, Pinyol R, Bertran MT, Regue L, Caelles C, Vernos I, Roig J", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "22818914", "url": "https://glygen.org/publication/PubMed/22818914" } ] }, { "title": "NEDD1-S411 phosphorylation plays a critical function in the coordination of microtubule nucleation during mitosis.", "journal": "Biology open", "date": "2022", "authors": "Timon Perez K, Scrofani J, Vernos I", "evidence": [ { "database": "RefSeq", "id": "NP_001128647", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001128647" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22818914", "url": "https://glygen.org/publication/PubMed/22818914", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MTSAMGKGTVAVQEKAGLPR", "down_seq": "INTDTLSKETDSGKNQDFSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q8TD19-1", "kinase_gene_name": "NEK9", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "22818914", "url": "https://glygen.org/publication/PubMed/22818914" } ], "site_lbl": "Ser377" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "22818914", "url": "https://glygen.org/publication/PubMed/22818914" }, { "database": "PubMed", "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115" } ], "site_lbl": "Ser377" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHV4-1.358.358", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHV4-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NHV4-1.397.397", "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": "Q8NHV4-1.382.382", "start_pos": 382, "end_pos": 382, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome.", "journal": "Journal of cell science", "date": "2009", "authors": "Zhang X, Chen Q, Feng J, Hou J, Yang F, Liu J, Jiang Q, Zhang C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GKGTVAVQEKAGLPRSINTD", "down_seq": "LSKETDSGKNQDFSSFDDTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P53350-1", "kinase_gene_name": "PLK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Thr382" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by PLK1", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Thr382" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8NHV4-1.377.377", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHV4-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHV4-1.397.397", "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": "Q8NHV4-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome.", "journal": "Journal of cell science", "date": "2009", "authors": "Zhang X, Chen Q, Feng J, Hou J, Yang F, Liu J, Jiang Q, Zhang C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ] }, { "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SINTDTLSKETDSGKNQDFS", "down_seq": "FDDTGKSSLGDMFSPIRDDA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P53350-1", "kinase_gene_name": "PLK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Ser397" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by PLK1", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ], "site_lbl": "Ser397" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NHV4-1.377.377", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8NHV4-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHV4-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHV4-1.405.405", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHV4-1.411.411", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.405.405", "start_pos": 405, "end_pos": 405, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Microtubule nucleation during central spindle assembly requires NEDD1 phosphorylation on serine 405 by Aurora A.", "journal": "Journal of cell science", "date": "2019", "authors": "Courtheoux T, Reboutier D, Vazeille T, Cremet JY, Benaud C, Vernos I, Prigent C", "evidence": [ { "database": "RefSeq", "id": "NP_001128647", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001128647" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "31028180", "url": "https://glygen.org/publication/PubMed/31028180" } ] }, { "title": "NEDD1-S411 phosphorylation plays a critical function in the coordination of microtubule nucleation during mitosis.", "journal": "Biology open", "date": "2022", "authors": "Timon Perez K, Scrofani J, Vernos I", "evidence": [ { "database": "RefSeq", "id": "NP_001128647", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001128647" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "31028180", "url": "https://glygen.org/publication/PubMed/31028180", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KETDSGKNQDFSSFDDTGKS", "down_seq": "LGDMFSPIRDDAVVNKGSDE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O14965-1", "kinase_gene_name": "AURKA", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "31028180", "url": "https://glygen.org/publication/PubMed/31028180" } ], "site_lbl": "Ser405" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115" } ], "site_lbl": "Ser405" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NHV4-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NHV4-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHV4-1.411.411", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHV4-1.423.423", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 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": "Q8NHV4-1.411.411", "start_pos": 411, "end_pos": 411, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "NEDD1-S411 phosphorylation plays a critical function in the coordination of microtubule nucleation during mitosis.", "journal": "Biology open", "date": "2022", "authors": "Timon Perez K, Scrofani J, Vernos I", "evidence": [ { "database": "RefSeq", "id": "NP_001128647", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001128647" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KNQDFSSFDDTGKSSLGDMF", "down_seq": "PIRDDAVVNKGSDESIGKGD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "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": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "36318115", "url": "https://glygen.org/publication/PubMed/36318115" } ], "site_lbl": "Ser411" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHV4-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHV4-1.405.405", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHV4-1.423.423", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHV4-1.426.426", "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": "Q8NHV4-1.423.423", "start_pos": 423, "end_pos": 423, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "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": "KSSLGDMFSPIRDDAVVNKG", "down_seq": "DESIGKGDGFDFLPQLNSVF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser423" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHV4-1.405.405", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8NHV4-1.411.411", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHV4-1.426.426", "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": "Q8NHV4-1.426.426", "start_pos": 426, "end_pos": 426, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome.", "journal": "Journal of cell science", "date": "2009", "authors": "Zhang X, Chen Q, Feng J, Hou J, Yang F, Liu J, Jiang Q, Zhang C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGDMFSPIRDDAVVNKGSDE", "down_seq": "IGKGDGFDFLPQLNSVFPPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P53350-1", "kinase_gene_name": "PLK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Ser426" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by PLK1", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Ser426" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHV4-1.411.411", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHV4-1.423.423", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 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": "Q8NHV4-1.468.468", "start_pos": 468, "end_pos": 468, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NPVTSSTSVLHSSPLNVFMG", "down_seq": "PGKEENENRDLTAESKKIYM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser468" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NHV4-1.460.460", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.515.515", "start_pos": 515, "end_pos": 515, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "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": "DSFKQLAKLVTSGAESGNLN", "down_seq": "SPSSNQTRNSEKFEKPENEI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Thr515" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8NHV4-1.506.506", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHV4-1.514.514", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHV4-1.516.516", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHV4-1.518.518", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NHV4-1.535.535", "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": "Q8NHV4-1.518.518", "start_pos": 518, "end_pos": 518, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "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": "KQLAKLVTSGAESGNLNTSP", "down_seq": "SNQTRNSEKFEKPENEIEAQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser518" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHV4-1.506.506", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHV4-1.514.514", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHV4-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHV4-1.516.516", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.535.535", "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": "Q8NHV4-1.550.550", "start_pos": 550, "end_pos": 550, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome.", "journal": "Journal of cell science", "date": "2009", "authors": "Zhang X, Chen Q, Feng J, Hou J, Yang F, Liu J, Jiang Q, Zhang C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KPENEIEAQLICEPPINGSS", "down_seq": "PNPKIASSVTAGVASSLSEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06493-1", "kinase_gene_name": "CDK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Thr550" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by CDK1", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Thr550" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHV4-1.535.535", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHV4-1.548.548", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHV4-1.557.557", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 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": "Q8NHV4-1.557.557", "start_pos": 557, "end_pos": 557, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Novel NEDD1 phosphorylation sites regulate gamma-tubulin binding and mitotic spindle assembly.", "journal": "Journal of cell science", "date": "2012", "authors": "Gomez-Ferreria MA, Bashkurov M, Helbig AO, Larsen B, Pawson T, Gingras AC, Pelletier L", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "22595525", "url": "https://glygen.org/publication/PubMed/22595525" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22595525", "url": "https://glygen.org/publication/PubMed/22595525", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AQLICEPPINGSSTPNPKIA", "down_seq": "SVTAGVASSLSEKIADSIGN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "22595525", "url": "https://glygen.org/publication/PubMed/22595525" } ], "site_lbl": "Ser557" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8NHV4-1.548.548", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHV4-1.550.550", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHV4-1.574.574", "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": "Q8NHV4-1.574.574", "start_pos": 574, "end_pos": 574, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis.", "journal": "Analytical chemistry", "date": "2008", "authors": "Wang B, Malik R, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] }, { "title": "Novel NEDD1 phosphorylation sites regulate gamma-tubulin binding and mitotic spindle assembly.", "journal": "Journal of cell science", "date": "2012", "authors": "Gomez-Ferreria MA, Bashkurov M, Helbig AO, Larsen B, Pawson T, Gingras AC, Pelletier L", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "22595525", "url": "https://glygen.org/publication/PubMed/22595525" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22595525", "url": "https://glygen.org/publication/PubMed/22595525", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIASSVTAGVASSLSEKIAD", "down_seq": "IGNNRQNAPLTSIQIRFIQN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" }, { "database": "PubMed", "id": "22595525", "url": "https://glygen.org/publication/PubMed/22595525" } ], "site_lbl": "Ser574" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHV4-1.557.557", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHV4-1.583.583", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHV4-1.590.590", "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": "Q8NHV4-1.637.637", "start_pos": 637, "end_pos": 637, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome.", "journal": "Journal of cell science", "date": "2009", "authors": "Zhang X, Chen Q, Feng J, Hou J, Yang F, Liu J, Jiang Q, Zhang C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" } ], "reference": [ { "type": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EMIKQFHMQLNEMHSLLERY", "down_seq": "VNEGLVAEIERLREENKRLR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P53350-1", "kinase_gene_name": "PLK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Ser637" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by PLK1", "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" }, { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "19509060", "url": "https://glygen.org/publication/PubMed/19509060" } ], "site_lbl": "Ser637" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8NHV4-1.641.641", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHV4-1.655.655", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHV4-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "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": "LLELAEGQKQTCVNLNSTSM", "down_seq": "LVSGGLNNTVNIWDLKSKRV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr91" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8NHV4-1.94.94", "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": "Q8NHV4-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "Q8NHV4-1", "length": 660, "uniprot_id": "NEDD1_HUMAN", "protein_name": "Protein NEDD1", "refseq_ac": "NP_001128647", "refseq_name": "protein NEDD1 isoform a", "gene_name": "NEDD1", "gene_names_uniprotkb": "NEDD1", "gene_names_refseq": "GCP-WD; NEDD1; TUBGCP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHV4", "url": "https://www.uniprot.org/uniprotkb/Q8NHV4" } ], "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": "Q8NHV4-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4", "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": "LAEGQKQTCVNLNSTSMYLV", "down_seq": "GGLNNTVNIWDLKSKRVHRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NHV4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHV4" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser94" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "348", "end_pos": "348" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "514", "end_pos": "514" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8NHV4-1.91.91", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A8MTL9-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "A8MTL9-1", "length": 139, "uniprot_id": "HMSD_HUMAN", "protein_name": "Serpin-like protein HMSD", "refseq_ac": "NP_001116838", "refseq_name": "serpin-like protein HMSD", "gene_name": "HMSD", "gene_names_uniprotkb": "HMSD; C18orf53", "gene_names_refseq": "ACC-6; ACC6; C18orf53; HMSD; HSMD-v", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A8MTL9", "url": "https://www.uniprot.org/uniprotkb/A8MTL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A8MTL9", "url": "https://www.uniprot.org/uniprotkb/A8MTL9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KIGGEDGDIHRGFQSLLVAI", "down_seq": "RTDTEYVLRTANGLFGEKSY", "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": "Asn50", "evidence": [ { "id": "A8MTL9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/A8MTL9#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "50", "end_pos": "50" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "A8MTL9-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "A8MTL9-1.51.51", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A8MTL9-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "A8MTL9-1", "length": 139, "uniprot_id": "HMSD_HUMAN", "protein_name": "Serpin-like protein HMSD", "refseq_ac": "NP_001116838", "refseq_name": "serpin-like protein HMSD", "gene_name": "HMSD", "gene_names_uniprotkb": "HMSD; C18orf53", "gene_names_refseq": "ACC-6; ACC6; C18orf53; HMSD; HSMD-v", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A8MTL9", "url": "https://www.uniprot.org/uniprotkb/A8MTL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs950210900", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs950210900", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs950210900", "url": "https://www.ncbi.nlm.nih.gov/snp/rs950210900#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs950210900", "url": "http://gnomad.broadinstitute.org/awesome?query=rs950210900", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QLDFVNDTEKSTTRVNSWVA", "down_seq": "KTKGENILLFYFDNILNSFI", "snv": [ { "evidence": [ { "id": "rs950210900", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs950210900" }, { "id": "rs950210900", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs950210900#frequency_tab" }, { "id": "rs950210900", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs950210900" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKT->NKT).", "chr_id": "18", "chr_pos": "63960263", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D110", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "50", "end_pos": "50" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "A8MTL9-1.123.123", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A8MTL9-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "A8MTL9-1", "length": 139, "uniprot_id": "HMSD_HUMAN", "protein_name": "Serpin-like protein HMSD", "refseq_ac": "NP_001116838", "refseq_name": "serpin-like protein HMSD", "gene_name": "HMSD", "gene_names_uniprotkb": "HMSD; C18orf53", "gene_names_refseq": "ACC-6; ACC6; C18orf53; HMSD; HSMD-v", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A8MTL9", "url": "https://www.uniprot.org/uniprotkb/A8MTL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A8MTL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RVNSWVADKTKGENILLFYF", "down_seq": "NILNSFIVSSLQNCQI", "snv": [ { "evidence": [ { "id": "A8MTL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "63960302", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D123", "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": "glycosylation", "site_list": [ { "start_pos": "50", "end_pos": "50" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "A8MTL9-1.110.110", "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": "A8MTL9-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "A8MTL9-1", "length": 139, "uniprot_id": "HMSD_HUMAN", "protein_name": "Serpin-like protein HMSD", "refseq_ac": "NP_001116838", "refseq_name": "serpin-like protein HMSD", "gene_name": "HMSD", "gene_names_uniprotkb": "HMSD; C18orf53", "gene_names_refseq": "ACC-6; ACC6; C18orf53; HMSD; HSMD-v", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A8MTL9", "url": "https://www.uniprot.org/uniprotkb/A8MTL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A8MTL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AQMSQALCFSKIGGEDGDIH", "down_seq": "GFQSLLVAINRTDTEYVLRT", "snv": [ { "evidence": [ { "id": "A8MTL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "63954453", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R40", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID: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": "50", "end_pos": "50" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "A8MTL9-1.50.50", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "A8MTL9-1.51.51", "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": "A8MTL9-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "A8MTL9-1", "length": 139, "uniprot_id": "HMSD_HUMAN", "protein_name": "Serpin-like protein HMSD", "refseq_ac": "NP_001116838", "refseq_name": "serpin-like protein HMSD", "gene_name": "HMSD", "gene_names_uniprotkb": "HMSD; C18orf53", "gene_names_refseq": "ACC-6; ACC6; C18orf53; HMSD; HSMD-v", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A8MTL9", "url": "https://www.uniprot.org/uniprotkb/A8MTL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A8MTL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IGGEDGDIHRGFQSLLVAIN", "down_seq": "TDTEYVLRTANGLFGEKSYD", "snv": [ { "evidence": [ { "id": "A8MTL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "63954487", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R51", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "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": "50", "end_pos": "50" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "A8MTL9-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "A8MTL9-1.50.50", "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": "A8MTL9-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "A8MTL9-1", "length": 139, "uniprot_id": "HMSD_HUMAN", "protein_name": "Serpin-like protein HMSD", "refseq_ac": "NP_001116838", "refseq_name": "serpin-like protein HMSD", "gene_name": "HMSD", "gene_names_uniprotkb": "HMSD; C18orf53", "gene_names_refseq": "ACC-6; ACC6; C18orf53; HMSD; HSMD-v", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A8MTL9", "url": "https://www.uniprot.org/uniprotkb/A8MTL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A8MTL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LRTANGLFGEKSYDFLTGFT", "down_seq": "SCGKFYQATIKQLDFVNDTE", "snv": [ { "evidence": [ { "id": "A8MTL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A8MTL9" } ], "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 (DSC->NSC).", "chr_id": "18", "chr_pos": "63960167", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D78", "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": "50", "end_pos": "50" } ] }, { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "51", "end_pos": "51" }, { "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05112-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Disulfide assignments in recombinant mouse and human interleukin 4.", "journal": "Biochemistry", "date": "1991", "authors": "Carr C, Aykent S, Kimack NM, Levine AD", "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112#ptm_processing" }, { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "reference": [ { "type": "PubMed", "id": "1993171", "url": "https://glygen.org/publication/PubMed/1993171" } ] } ], "crossref": [ { "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "1993171", "url": "https://glygen.org/publication/PubMed/1993171", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TEQKTLCTELTVTDIFAASK", "down_seq": "TTEKETFCRAATVLRQFYSH", "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": "Asn62", "evidence": [ { "id": "P05112", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05112#ptm_processing" }, { "id": "1993171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/1993171" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P05112-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05112-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05112-1.64.64", "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": "P05112-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A pathological role of O-GlcNAcylation-driven TR11B production and function in lung adenocarcinoma.", "journal": "Developmental cell", "date": "2025-12-01", "authors": "Qiu Shiyu, Ma Lifang, Yu Keke, Xu Xin, Zhang Xiao, Yu Wenjun, Wang Kai, Tian Xiaoting, Miao Yayou, Wang Yikun, Guo Wanxin, Xue Xiangfei, Cui Jiangtao, Yu Xuewen, Kang Rui, Zhou Qianjun, Yu Yongchun, Tang Daolin, Wang Jiayi", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05112", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05112" } ], "reference": [ { "type": "PubMed", "id": "40930100", "url": "https://glygen.org/publication/PubMed/40930100" } ] }, { "title": "The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of clinical immunologists from China.", "journal": "Clinical immunology (Orlando, Fla.)", "date": "2020", "authors": "Zhang W, Zhao Y, Zhang F, Wang Q, Li T, Liu Z, Wang J, Qin Y, Zhang X, Yan X, Zeng X, Zhang S", "evidence": [ { "database": "BiomarkerKB", "id": "AN6334-1", "url": "https://biomarkerkb.org/biomarker/AN6334-1" } ], "reference": [ { "type": "PubMed", "id": "32222466", "url": "https://glygen.org/publication/PubMed/32222466" } ] }, { "title": "VEGF-D: a novel biomarker for detection of COVID-19 progression.", "journal": "Critical care (London, England)", "date": "2020", "authors": "Kong Y, Han J, Wu X, Zeng H, Liu J, Zhang H", "evidence": [ { "database": "BiomarkerKB", "id": "AN6334-1", "url": "https://biomarkerkb.org/biomarker/AN6334-1" } ], "reference": [ { "type": "PubMed", "id": "32576222", "url": "https://glygen.org/publication/PubMed/32576222" } ] }, { "title": "Clinical investigation of the role of interleukin-4 and interleukin-13 in the evolution of prostate cancer.", "journal": "Cancers", "date": "2011", "authors": "Goldstein R, Hanley C, Morris J, Cahill D, Chandra A, Harper P, Chowdhury S, Maher J, Burbridge S", "evidence": [ { "database": "BiomarkerKB", "id": "AN6334-2", "url": "https://biomarkerkb.org/biomarker/AN6334-2" } ], "reference": [ { "type": "PubMed", "id": "24213139", "url": "https://glygen.org/publication/PubMed/24213139" } ] } ], "crossref": [ { "id": "40930100", "url": "https://glygen.org/publication/PubMed/40930100", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P05112", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05112", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "AN6334-1", "url": "https://biomarkerkb.org/biomarker/AN6334-1", "database": "BiomarkerKB", "categories": [ "Biomarkers" ] }, { "id": "32222466", "url": "https://glygen.org/publication/PubMed/32222466", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32576222", "url": "https://glygen.org/publication/PubMed/32576222", "database": "PubMed", "categories": [ "Other" ] }, { "id": "AN6334-2", "url": "https://biomarkerkb.org/biomarker/AN6334-2", "database": "BiomarkerKB", "categories": [ "Biomarkers" ] }, { "id": "24213139", "url": "https://glygen.org/publication/PubMed/24213139", "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": "40930100", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40930100" }, { "id": "P05112", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05112" } ] } ], "biomarkers": [ { "biomarker_id": "AN6334-1", "biomarker_canonical_id": "AN6334", "best_biomarker_role": [ "monitoring" ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "name_list": [ "COVID-19", "2019 Novel Coronavirus (2019-nCoV)", "2019-nCoV infection", "COVID19", "SARS-CoV-2 infection", "2019 novel coronavirus infection", "coronavirus disease 2019", "severe acute respiratory syndrome coronavirus 2 infectious disease", "2019 novel coronavirus", "2019-nCoV", "SARS-CoV-2", "SARS-coronavirus 2", "beta-CoV", "beta-CoVs", "betacoronavirus", "severe acute respiratory syndrome coronavirus 2", "-CoV", "-CoVs", "-coronavirus" ], "id_list": [ "DOID:0080600", "MONDO:0100096" ] }, "evidence": [ { "id": "AN6334-1", "database": "BiomarkerKB", "url": "https://biomarkerkb.org/biomarker/AN6334-1" }, { "id": "32222466", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32222466" }, { "id": "32576222", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32576222" } ], "assessed_biomarker_entity": [ "Interleukin-4" ], "biomarker": [ "increased IL4 level" ] }, { "biomarker_id": "AN6334-2", "biomarker_canonical_id": "AN6334", "best_biomarker_role": [ "monitoring" ], "condition": { "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." }, "name_list": [ "prostate cancer", "NGP - new growth of prostate", "hereditary prostate cancer", "malignant tumor of the prostate", "prostate cancer, familial", "prostate neoplasm", "prostatic cancer", "prostatic neoplasm", "tumor of the prostate", "prostate cancer, hereditary, X-linked 1", "HPCX1", "prostate cancer, hereditary, X-linked 2", "HPCX2", "prostate cancer, hereditary, 1", "RNASEL familial prostate cancer", "familial prostate cancer caused by mutation in RNASEL", "prostate cancer 1", "prostate cancer, hereditary, type 1", "HPC1", "prostate cancer, hereditary, 8", "prostate cancer, hereditary, type 8", "HPC8", "prostate cancer, hereditary, 3", "prostate cancer, hereditary, type 3", "prostate cancer, susceptibility to, 3", "HPC3", "prostate cancer, hereditary, 4", "prostate cancer, hereditary, type 4", "prostate cancer, susceptibility to, 4", "HPC4", "prostate cancer, hereditary, 5", "prostate cancer, hereditary, type 5", "HPC5", "prostate cancer, hereditary, 6", "prostate cancer, hereditary, type 6", "HPC6", "prostate cancer, hereditary, 7", "HPC7", "prostate cancer, hereditary, 9", "prostate cancer, hereditary, type 9", "HPC9", "prostate cancer, hereditary, 10", "HPC10", "prostate cancer, hereditary, 12", "EHBP1 familial prostate cancer", "familial prostate cancer caused by mutation in EHBP1", "prostate cancer, hereditary, type 12", "HPC12", "prostate cancer, hereditary, 13", "MSMB familial prostate cancer", "familial prostate cancer caused by mutation in MSMB", "prostate cancer, hereditary, type 13", "HPC13", "prostate cancer, hereditary, 11", "HPC11", "prostate cancer, hereditary, 14", "HPC14", "prostate cancer, hereditary, 15", "HPC15", "prostate cancer, hereditary", "Prostate cancer, hereditary, 1", "Prostate cancer, hereditary, 9", "Prostate cancer, hereditary, 12", "Prostate cancer, hereditary, 13", "Prostate cancer, hereditary, 11", "Prostate cancer" ], "id_list": [ "DOID:10283", "MONDO:0010257", "MONDO:0010405", "MONDO:0011098", "MONDO:0011270", "MONDO:0012093", "MONDO:0012094", "MONDO:0012244", "MONDO:0012300", "MONDO:0012470", "MONDO:0012597", "MONDO:0012620", "MONDO:0012741", "MONDO:0012758", "MONDO:0012768", "MONDO:0012769", "MONDO:0012770", "MONDO:0700275", "MIM:601518", "MIM:610997", "MIM:611868", "MIM:611928", "MIM:611955", "MIM:176807" ] }, "evidence": [ { "id": "AN6334-2", "database": "BiomarkerKB", "url": "https://biomarkerkb.org/biomarker/AN6334-2" }, { "id": "24213139", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24213139" } ], "assessed_biomarker_entity": [ "Interleukin-4" ], "biomarker": [ "increased IL4 level" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "glycosylation_flag", "biomarkers_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "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": "P05112-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of interleukin 4 mutant E9A suggests polar steering in receptor-complex formation.", "journal": "Acta crystallographica. Section D, Biological crystallography", "date": "2001", "authors": "Hulsmeyer M, Scheufler C, Dreyer MK", "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "reference": [ { "type": "PubMed", "id": "11526337", "url": "https://glygen.org/publication/PubMed/11526337" } ] } ], "crossref": [ { "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11526337", "url": "https://glygen.org/publication/PubMed/11526337", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "FLLACAGNFVHGHKCDITLQ", "down_seq": "IIKTLNSLTEQKTLCTELTV", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "About 500-fold lower interaction with IL4R than WT.", "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" }, { "database": "PubMed", "id": "11526337", "url": "https://glygen.org/publication/PubMed/11526337" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P05112-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05112-1.53.53", "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": "P05112-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1752453287", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1752453287", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1752453287", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1752453287#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "QQFHRHKQLIRFLKRLDRNL", "down_seq": "GLAGLNSCPVKEANQSTLEN", "snv": [ { "evidence": [ { "id": "rs1752453287", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1752453287" }, { "id": "rs1752453287", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1752453287#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLW->NLC).", "chr_id": "5", "chr_pos": "132679875", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W115", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05112-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05112", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs772721636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772721636", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772721636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772721636", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772721636", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772721636#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772721636", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772721636", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs772721636", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772721636", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LPPLFFLLACAGNFVHGHKC", "down_seq": "ITLQEIIKTLNSLTEQKTLC", "snv": [ { "evidence": [ { "id": "P05112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05112" }, { "id": "rs772721636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772721636" }, { "id": "rs772721636", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772721636" }, { "id": "rs772721636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772721636#frequency_tab" }, { "id": "rs772721636", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772721636" }, { "id": "rs772721636", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772721636" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DIT->NIT).", "chr_id": "5", "chr_pos": "132674132", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D28", "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": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P05112-1.33.33", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05112-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05112", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EIIKTLNSLTEQKTLCTELT", "down_seq": "TDIFAASKNTTEKETFCRAA", "snv": [ { "evidence": [ { "id": "P05112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05112" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "132674480", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V53", "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": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05112-1.33.33", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P05112-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P05112-1.62.62", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P05112-1.64.64", "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": "P05112-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05112", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LTEQKTLCTELTVTDIFAAS", "down_seq": "NTTEKETFCRAATVLRQFYS", "snv": [ { "evidence": [ { "id": "P05112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05112" } ], "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 (KNT->NNT).", "chr_id": "5", "chr_pos": "132674506", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K61", "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": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P05112-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05112-1.62.62", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P05112-1.64.64", "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": "P05112-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P05112-1", "length": 153, "uniprot_id": "IL4_HUMAN", "protein_name": "Interleukin-4", "refseq_ac": "NP_000580", "refseq_name": "interleukin-4 isoform 1 precursor", "gene_name": "IL4", "gene_names_uniprotkb": "IL4", "gene_names_refseq": "BCGF-1; BCGF1; BSF-1; BSF1; IL-4; IL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05112", "url": "https://www.uniprot.org/uniprotkb/P05112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs199591873", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199591873", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199591873", "url": "https://www.ensembl.org/id/rs199591873", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1047696325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047696325", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1047696325", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1047696325", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QKTLCTELTVTDIFAASKNT", "down_seq": "EKETFCRAATVLRQFYSHHE", "snv": [ { "evidence": [ { "id": "rs199591873", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199591873" }, { "id": "rs199591873", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs199591873" } ], "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 (NTT->NTA).", "chr_id": "5", "chr_pos": "132679720", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T64", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1047696325", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047696325" }, { "id": "rs1047696325", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1047696325" } ], "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": "5", "chr_pos": "132679721", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T64", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1047696325", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047696325" }, { "id": "rs1047696325", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1047696325" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->NTN).", "chr_id": "5", "chr_pos": "132679721", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T64", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "62", "end_pos": "62" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "64", "end_pos": "64" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P05112-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P05112-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P05112-1.62.62", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "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": "P05187-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "Structural studies of human alkaline phosphatase in complex with strontium: implication for its secondary effect in bones.", "journal": "Protein science : a publication of the Protein Society", "date": "2006", "authors": "Llinas P, Masella M, Stigbrand T, Menez A, Stura EA, Le Du MH", "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "reference": [ { "type": "PubMed", "id": "16815919", "url": "https://glygen.org/publication/PubMed/16815919" } ] }, { "title": "Structural studies of human placental alkaline phosphatase in complex with functional ligands.", "journal": "Journal of molecular biology", "date": "2005", "authors": "Llinas P, Stura EA, Menez A, Kiss Z, Stigbrand T, Millan JL, Le Du MH", "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "reference": [ { "type": "PubMed", "id": "15946677", "url": "https://glygen.org/publication/PubMed/15946677" } ] }, { "title": "Refined structures of placental alkaline phosphatase show a consistent pattern of interactions at the peripheral site.", "journal": "Acta crystallographica. Section F, Structural biology and crystallization communications", "date": "2010", "authors": "Stec B, Cheltsov A, Millan JL", "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" }, { "database": "RefSeq", "id": "NP_001623", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001623" } ], "reference": [ { "type": "PubMed", "id": "20693656", "url": "https://glygen.org/publication/PubMed/20693656" } ] } ], "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": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16815919", "url": "https://glygen.org/publication/PubMed/16815919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15946677", "url": "https://glygen.org/publication/PubMed/15946677", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20693656", "url": "https://glygen.org/publication/PubMed/20693656", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1EW2", "url": "https://www.rcsb.org/structure/1EW2", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1ZEB", "url": "https://www.rcsb.org/structure/1ZEB", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1ZED", "url": "https://www.rcsb.org/structure/1ZED", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2GLQ", "url": "https://www.rcsb.org/structure/2GLQ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1ZEF", "url": "https://www.rcsb.org/structure/1ZEF", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1EW2|A|122", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "1ZEB|A|122", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "1ZED|A|122", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2GLQ|A|122", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "1ZEF|A|122", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs1170744134", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170744134", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1170744134", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1170744134#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1170744134", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170744134", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GVKGNFQTIGLSAAARFNQC", "down_seq": "TTRGNEVISVMNRAKKAGKS", "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": "FNQCNTTR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn144", "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": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=1EW2&bu=0&command=select+.A:122;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn144", "evidence": [ { "id": "P05187", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "id": "16815919", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16815919" }, { "id": "15946677", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/15946677" }, { "id": "20693656", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20693656" }, { "id": "1EW2", "database": "PDB", "url": "https://www.rcsb.org/structure/1EW2" }, { "id": "1ZEB", "database": "PDB", "url": "https://www.rcsb.org/structure/1ZEB" }, { "id": "1ZED", "database": "PDB", "url": "https://www.rcsb.org/structure/1ZED" }, { "id": "2GLQ", "database": "PDB", "url": "https://www.rcsb.org/structure/2GLQ" }, { "id": "1ZEF", "database": "PDB", "url": "https://www.rcsb.org/structure/1ZEF" } ] } ], "snv": [ { "evidence": [ { "id": "rs1170744134", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170744134" }, { "id": "rs1170744134", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1170744134#frequency_tab" }, { "id": "rs1170744134", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170744134" } ], "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": "2", "chr_pos": "232379633", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N144", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P05187-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05187-1.146.146", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 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", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05187-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural studies of human alkaline phosphatase in complex with strontium: implication for its secondary effect in bones.", "journal": "Protein science : a publication of the Protein Society", "date": "2006", "authors": "Llinas P, Masella M, Stigbrand T, Menez A, Stura EA, Le Du MH", "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "reference": [ { "type": "PubMed", "id": "16815919", "url": "https://glygen.org/publication/PubMed/16815919" } ] }, { "title": "Structural studies of human placental alkaline phosphatase in complex with functional ligands.", "journal": "Journal of molecular biology", "date": "2005", "authors": "Llinas P, Stura EA, Menez A, Kiss Z, Stigbrand T, Millan JL, Le Du MH", "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "reference": [ { "type": "PubMed", "id": "15946677", "url": "https://glygen.org/publication/PubMed/15946677" } ] }, { "title": "Refined structures of placental alkaline phosphatase show a consistent pattern of interactions at the peripheral site.", "journal": "Acta crystallographica. Section F, Structural biology and crystallization communications", "date": "2010", "authors": "Stec B, Cheltsov A, Millan JL", "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" }, { "database": "RefSeq", "id": "NP_001623", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001623" } ], "reference": [ { "type": "PubMed", "id": "20693656", "url": "https://glygen.org/publication/PubMed/20693656" } ] } ], "crossref": [ { "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16815919", "url": "https://glygen.org/publication/PubMed/16815919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15946677", "url": "https://glygen.org/publication/PubMed/15946677", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20693656", "url": "https://glygen.org/publication/PubMed/20693656", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1ZEB", "url": "https://www.rcsb.org/structure/1ZEB", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1ZED", "url": "https://www.rcsb.org/structure/1ZED", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2GLQ", "url": "https://www.rcsb.org/structure/2GLQ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1ZEF", "url": "https://www.rcsb.org/structure/1ZEF", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1ZEB|A|249", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "1ZED|A|249", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2GLQ|A|249", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "1ZEF|A|249", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1235031507", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235031507", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1235031507", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1235031507#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1235031507", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235031507", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DGKNLVQEWLAKRQGARYVW", "down_seq": "RTELMQASLDPSVTHLMGLF", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=1ZEB&bu=0&command=select+.A:249;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn271", "evidence": [ { "id": "P05187", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05187#ptm_processing" }, { "id": "16815919", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16815919" }, { "id": "15946677", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/15946677" }, { "id": "20693656", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20693656" }, { "id": "1ZEB", "database": "PDB", "url": "https://www.rcsb.org/structure/1ZEB" }, { "id": "1ZED", "database": "PDB", "url": "https://www.rcsb.org/structure/1ZED" }, { "id": "2GLQ", "database": "PDB", "url": "https://www.rcsb.org/structure/2GLQ" }, { "id": "1ZEF", "database": "PDB", "url": "https://www.rcsb.org/structure/1ZEF" } ] } ], "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" }, { "id": "rs1235031507", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235031507" }, { "id": "rs1235031507", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1235031507#frequency_tab" }, { "id": "rs1235031507", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235031507" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NRT->KRT).", "chr_id": "2", "chr_pos": "232380440", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "N271", "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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P05187-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P05187-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05187-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05187-1.273.273", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P05187-1.283.283", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05187-1.513.513", "start_pos": 513, "end_pos": 513, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-Linked N-Acetylglucosamine Transferase Regulates Bone Homeostasis Through Alkaline Phosphatase Pathway in Diabetic Periodontitis.", "journal": "Molecular biotechnology", "date": "2023-11-11", "authors": "Luo Wei, Sun Lu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P05187", "url": "https://oglcnac.org/atlas/detail/P05187" }, { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "37951846", "url": "https://glygen.org/publication/PubMed/37951846" } ] } ], "crossref": [ { "id": "37951846", "url": "https://glygen.org/publication/PubMed/37951846", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P05187", "url": "https://oglcnac.org/atlas/detail/P05187", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1696719859", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1696719859", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1696719859", "url": "https://www.ensembl.org/id/rs1696719859", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YTACDLAPPAGTTDAAHPGR", "down_seq": "VVPALLPLLAGTLLLLETAT", "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": "Ser513", "evidence": [ { "id": "37951846", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37951846" }, { "id": "P05187", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P05187" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "automatic_literature_mining", "site_category_dict": { "automatic_literature_mining": true }, "site_seq": "S", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser513", "evidence": [ { "id": "37951846", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37951846" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "snv": [ { "evidence": [ { "id": "rs1696719859", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1696719859" }, { "id": "rs1696719859", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1696719859" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "2", "chr_pos": "232381725", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S513", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P05187-1.512.512", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P05187-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TAYLCGVKGNFQTIGLSAAA", "down_seq": "FNQCNTTRGNEVISVMNRAK", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "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": "2", "chr_pos": "232379618", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R139", "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: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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05187-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P05187-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P05187-1.146.146", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs146026871", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146026871", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs146026871", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146026871", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs146026871", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146026871", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KGNFQTIGLSAAARFNQCNT", "down_seq": "RGNEVISVMNRAKKAGKSVG", "snv": [ { "evidence": [ { "id": "rs146026871", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146026871" }, { "id": "rs146026871", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146026871" }, { "id": "rs146026871", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146026871" } ], "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": "2", "chr_pos": "232379640", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T146", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P05187-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P05187-1.144.144", "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": "P05187-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1269117429", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269117429", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1269117429", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1269117429#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1269117429", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269117429", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NEVISVMNRAKKAGKSVGVV", "down_seq": "TTRVQHASPAGTYAHTVNRN", "snv": [ { "evidence": [ { "id": "rs1269117429", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269117429" }, { "id": "rs1269117429", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1269117429#frequency_tab" }, { "id": "rs1269117429", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269117429" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TTT->NTT).", "chr_id": "2", "chr_pos": "232379785", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T169", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "P05187-1.189.189", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1487377668", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1487377668", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1487377668", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1487377668#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1487377668", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1487377668", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TTTRVQHASPAGTYAHTVNR", "down_seq": "WYSDADVPASARQEGCQDIA", "snv": [ { "evidence": [ { "id": "rs1487377668", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1487377668" }, { "id": "rs1487377668", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1487377668#frequency_tab" }, { "id": "rs1487377668", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1487377668" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRN->NRS).", "chr_id": "2", "chr_pos": "232379845", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N189", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05187-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05187-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P05187-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05187-1.209.209", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1696672025", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1696672025", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1696672025", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1696672025#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TRVQHASPAGTYAHTVNRNW", "down_seq": "SDADVPASARQEGCQDIATQ", "snv": [ { "evidence": [ { "id": "rs1696672025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1696672025" }, { "id": "rs1696672025", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1696672025#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NWY->NWS).", "chr_id": "2", "chr_pos": "232379851", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y191", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P05187-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P05187-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P05187-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P05187-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TYAHTVNRNWYSDADVPASA", "down_seq": "QEGCQDIATQLISNMDIDVI", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "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": "2", "chr_pos": "232379881", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R201", "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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P05187-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P05187-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P05187-1.209.209", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P05187-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NWYSDADVPASARQEGCQDI", "down_seq": "TQLISNMDIDVILGGGRKYM", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "232379904", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A209", "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: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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05187-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P05187-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P05187-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05187-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "WYSDADVPASARQEGCQDIA", "down_seq": "QLISNMDIDVILGGGRKYMF", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "232379908", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T210", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P05187-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P05187-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05187-1.209.209", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QLISNMDIDVILGGGRKYMF", "down_seq": "MGTPDPEYPDDYSQGGTRLD", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "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": "2", "chr_pos": "232380219", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R231", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DDYSQGGTRLDGKNLVQEWL", "down_seq": "KRQGARYVWNRTELMQASLD", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "232380310", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A261", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P05187-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P05187-1.271.271", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P05187-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P05187-1.273.273", "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": "P05187-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YSQGGTRLDGKNLVQEWLAK", "down_seq": "QGARYVWNRTELMQASLDPS", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "2", "chr_pos": "232380315", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R263", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "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": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "232380316", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R263", "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: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": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P05187-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P05187-1.271.271", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P05187-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P05187-1.273.273", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05187-1.283.283", "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": 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": "P05187-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs148586042", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148586042", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148586042", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148586042", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148586042", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148586042#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148586042", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148586042", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GKNLVQEWLAKRQGARYVWN", "down_seq": "TELMQASLDPSVTHLMGLFE", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "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": "2", "chr_pos": "232380442", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R272", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs148586042", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148586042" }, { "id": "rs148586042", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148586042" }, { "id": "rs148586042", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148586042#frequency_tab" }, { "id": "rs148586042", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148586042" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->NPT).", "chr_id": "2", "chr_pos": "232380442", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R272", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P05187-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P05187-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05187-1.271.271", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05187-1.273.273", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P05187-1.283.283", "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": 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": "P05187-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "rs1225894542", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225894542", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225894542", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225894542", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1307945599", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1307945599", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1307945599", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1307945599#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1307945599", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1307945599", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KNLVQEWLAKRQGARYVWNR", "down_seq": "ELMQASLDPSVTHLMGLFEP", "snv": [ { "evidence": [ { "id": "rs1225894542", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225894542" }, { "id": "rs1225894542", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225894542" } ], "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 (NRT->NRA).", "chr_id": "2", "chr_pos": "232380444", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T273", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1307945599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1307945599" }, { "id": "rs1307945599", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1307945599#frequency_tab" }, { "id": "rs1307945599", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1307945599" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->NRN).", "chr_id": "2", "chr_pos": "232380445", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T273", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Thr273" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P05187-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P05187-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P05187-1.271.271", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05187-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P05187-1.283.283", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05187-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MGLFEPGDMKYEIHRDSTLD", "down_seq": "SLMEMTEAALRLLSRNPRGF", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "232380680", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P308", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P05187-1.314.314", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P05187-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EIHRDSTLDPSLMEMTEAAL", "down_seq": "LLSRNPRGFFLFVEGGRIDH", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "2", "chr_pos": "232380712", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R319", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID: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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P05187-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P05187-1.314.314", "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": "P05187-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1260419831", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260419831", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1260419831", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1260419831#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1260419831", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260419831", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SRNPRGFFLFVEGGRIDHGH", "down_seq": "ESRAYRALTETIMFDDAIER", "snv": [ { "evidence": [ { "id": "rs1260419831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260419831" }, { "id": "rs1260419831", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1260419831#frequency_tab" }, { "id": "rs1260419831", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260419831" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HES->NES).", "chr_id": "2", "chr_pos": "232380863", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H342", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.379.379", "start_pos": 379, "end_pos": 379, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1393887224", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1393887224", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1393887224", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1393887224", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AIERAGQLTSEEDTLSLVTA", "down_seq": "HSHVFSFGGYPLRGSSIFGL", "snv": [ { "evidence": [ { "id": "rs1393887224", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1393887224" }, { "id": "rs1393887224", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1393887224" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DHS->NHS).", "chr_id": "2", "chr_pos": "232380974", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D379", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2469514560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2469514560", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YTVLLYGNGPGYVLKDGARP", "down_seq": "VTESESGSPEYRQQSAVPLD", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" }, { "id": "rs2469514560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2469514560" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "2", "chr_pos": "232381346", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D430", "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": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05187-1.410.410", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P05187-1.415.415", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P05187-1.421.421", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P05187-1.435.435", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "YGNGPGYVLKDGARPDVTES", "down_seq": "SGSPEYRQQSAVPLDEETHA", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "232381361", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E435", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05187-1.415.415", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P05187-1.421.421", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P05187-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P05187-1.451.451", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.451.451", "start_pos": 451, "end_pos": 451, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VTESESGSPEYRQQSAVPLD", "down_seq": "ETHAGEDVAVFARGPQAHLV", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "232381539", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "E451", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P05187-1.435.435", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.512.512", "start_pos": 512, "end_pos": 512, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05187", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PYTACDLAPPAGTTDAAHPG", "down_seq": "SVVPALLPLLAGTLLLLETA", "snv": [ { "evidence": [ { "id": "P05187", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05187" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "2", "chr_pos": "232381722", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R512", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P05187-1.513.513", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05187-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "DRFPYVALSKTYNVDKHVPD", "down_seq": "GATATAYLCGVKGNFQTIGL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser114" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P05187-1.117.117", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P05187-1.119.119", "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": "P05187-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "PYVALSKTYNVDKHVPDSGA", "down_seq": "ATAYLCGVKGNFQTIGLSAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr117" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P05187-1.114.114", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05187-1.119.119", "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": "P05187-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "VALSKTYNVDKHVPDSGATA", "down_seq": "AYLCGVKGNFQTIGLSAAAR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr119" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P05187-1.114.114", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P05187-1.117.117", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05187-1.139.139", "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": "P05187-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "RQGARYVWNRTELMQASLDP", "down_seq": "VTHLMGLFEPGDMKYEIHRD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser283" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05187-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P05187-1.271.271", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P05187-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P05187-1.273.273", "categories": [ "snv_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05187-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "GDMKYEIHRDSTLDPSLMEM", "down_seq": "EAALRLLSRNPRGFFLFVEG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr314" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P05187-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P05187-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05187-1.410.410", "start_pos": 410, "end_pos": 410, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "PLRGSSIFGLAPGKARDRKA", "down_seq": "TVLLYGNGPGYVLKDGARPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr410" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P05187-1.415.415", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P05187-1.421.421", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05187-1.430.430", "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": "P05187-1.415.415", "start_pos": 415, "end_pos": 415, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "SIFGLAPGKARDRKAYTVLL", "down_seq": "GNGPGYVLKDGARPDVTESE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr415" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P05187-1.410.410", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P05187-1.421.421", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P05187-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05187-1.435.435", "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": "P05187-1.421.421", "start_pos": 421, "end_pos": 421, "uniprot_canonical_ac": "P05187-1", "length": 535, "uniprot_id": "PPB1_HUMAN", "protein_name": "Alkaline phosphatase, placental type", "refseq_ac": "NP_001623", "refseq_name": "alkaline phosphatase, placental type preproprotein", "gene_name": "ALPP", "gene_names_uniprotkb": "ALPP; PLAP", "gene_names_refseq": "ALPP; ALP; PALP; PLAP-1; PLAP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05187", "url": "https://www.uniprot.org/uniprotkb/P05187" } ], "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": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187", "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": "PGKARDRKAYTVLLYGNGPG", "down_seq": "VLKDGARPDVTESESGSPEY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P05187", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05187" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr421" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "144", "end_pos": "144" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P05187-1.410.410", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P05187-1.415.415", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P05187-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P05187-1.435.435", "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": "O60671-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "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": "QQIQDEDDQYSLVASLDNVR", "down_seq": "LSTILKAIHFREHATCFATK", "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": "NLSTILK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn26", "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": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O60671-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O60671-1.28.28", "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": "O60671-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "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": "rs779740844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779740844", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779740844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779740844", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779740844", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779740844", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IQAGIFQEFKVQEESVTFRI", "down_seq": "LTVLLDCLSIFGSSPMPGTL", "glycosylation": [ { "glytoucan_ac": "G43591AT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "INLTVLLDCLSIFGSSPMPGTLTALR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn85", "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": "rs779740844", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779740844" }, { "id": "rs779740844", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779740844" }, { "id": "rs779740844", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779740844" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->KLT).", "chr_id": "5", "chr_pos": "34913522", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N85", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O60671-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O60671-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O60671-1.98.98", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O60671-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.", "journal": "The Journal of biological chemistry", "date": "2020-01-24", "authors": "Hara Kodai, Iida Nao, Tamafune Ryota, Ohashi Eiji, Sakurai Hitomi, Ishikawa Yoshinobu, Hishiki Asami, Hashimoto Hiroshi", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "reference": [ { "type": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "crossref": [ { "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NTQEPEETLDFDFCSTNVIN", "down_seq": "IILQSEGLREAFSELDMTSE", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Reduced binding to RHNO1; when associated with A-244 and A-254.", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" }, { "database": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O60671-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O60671-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O60671-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O60671-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O60671-1.173.173", "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": "O60671-1.226.233", "start_pos": 226, "end_pos": 233, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The human checkpoint protein hRad17 interacts with the PCNA-like proteins hRad1, hHus1, and hRad9.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Rauen M, Burtelow MA, Dufault VM, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "reference": [ { "type": "PubMed", "id": "10884395", "url": "https://glygen.org/publication/PubMed/10884395" } ] } ], "crossref": [ { "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10884395", "url": "https://glygen.org/publication/PubMed/10884395", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "SLLKPSTK", "start_aa": "S", "up_seq": "DSDLMEAFHCNQTQVNRYKI", "down_seq": "ALVLSCKVSIRTDNRGFLSL", "mutagenesis": [ { "sequence_org": "SLLKPSTK", "sequence_mut": "AAAAAAAA", "comment": "Abolishes association of the 9-1-1 complex with RAD17.", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" }, { "database": "PubMed", "id": "10884395", "url": "https://glygen.org/publication/PubMed/10884395" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O60671-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O60671-1.244.244", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O60671-1.249.249", "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": "O60671-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.", "journal": "The Journal of biological chemistry", "date": "2020-01-24", "authors": "Hara Kodai, Iida Nao, Tamafune Ryota, Ohashi Eiji, Sakurai Hitomi, Ishikawa Yoshinobu, Hishiki Asami, Hashimoto Hiroshi", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "reference": [ { "type": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "crossref": [ { "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KISLLKPSTKALVLSCKVSI", "down_seq": "TDNRGFLSLQYMIRNEDGQI", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Reduced binding to RHNO1; when associated with A-155 and A-254.", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" }, { "database": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O60671-1.226.233", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O60671-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O60671-1.254.254", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O60671-1.256.256", "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": "O60671-1.254.254", "start_pos": 254, "end_pos": 254, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.", "journal": "The Journal of biological chemistry", "date": "2020-01-24", "authors": "Hara Kodai, Iida Nao, Tamafune Ryota, Ohashi Eiji, Sakurai Hitomi, Ishikawa Yoshinobu, Hishiki Asami, Hashimoto Hiroshi", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "reference": [ { "type": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "crossref": [ { "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ALVLSCKVSIRTDNRGFLSL", "down_seq": "YMIRNEDGQICFVEYYCCPD", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Reduced binding to RHNO1; when associated with A-155 and A-244.", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" }, { "database": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O60671-1.244.244", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O60671-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O60671-1.256.256", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O60671-1.266.266", "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": "O60671-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.", "journal": "The Journal of biological chemistry", "date": "2020-01-24", "authors": "Hara Kodai, Iida Nao, Tamafune Ryota, Ohashi Eiji, Sakurai Hitomi, Ishikawa Yoshinobu, Hishiki Asami, Hashimoto Hiroshi", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "reference": [ { "type": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "crossref": [ { "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "VLSCKVSIRTDNRGFLSLQY", "down_seq": "IRNEDGQICFVEYYCCPDEE", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "A", "comment": "Reduced binding to RHNO1; when associated with A-64 and A-266.", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" }, { "database": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O60671-1.244.244", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O60671-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O60671-1.254.254", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O60671-1.266.266", "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": "O60671-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.", "journal": "The Journal of biological chemistry", "date": "2020-01-24", "authors": "Hara Kodai, Iida Nao, Tamafune Ryota, Ohashi Eiji, Sakurai Hitomi, Ishikawa Yoshinobu, Hishiki Asami, Hashimoto Hiroshi", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "reference": [ { "type": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "crossref": [ { "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "DNRGFLSLQYMIRNEDGQIC", "down_seq": "VEYYCCPDEEVPESES", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Reduced binding to RHNO1; when associated with A-64 and A-256.", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" }, { "database": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O60671-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O60671-1.254.254", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O60671-1.256.256", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O60671-1.281.281", "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": "O60671-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.", "journal": "The Journal of biological chemistry", "date": "2020-01-24", "authors": "Hara Kodai, Iida Nao, Tamafune Ryota, Ohashi Eiji, Sakurai Hitomi, Ishikawa Yoshinobu, Hishiki Asami, Hashimoto Hiroshi", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "reference": [ { "type": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "crossref": [ { "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "ATKNGIKVTVENAKCVQANA", "down_seq": "IQAGIFQEFKVQEESVTFRI", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Reduced binding to RHNO1; when associated with A-256 and A-266.", "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" }, { "database": "PubMed", "id": "31776186", "url": "https://glygen.org/publication/PubMed/31776186" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "O60671-1.83.83", "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": "O60671-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs145810279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145810279", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145810279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145810279", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145810279", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145810279#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145810279", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145810279", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GGVVTVCKINTQEPEETLDF", "down_seq": "FCSTNVINKIILQSEGLREA", "snv": [ { "evidence": [ { "id": "rs145810279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145810279" }, { "id": "rs145810279", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145810279" }, { "id": "rs145810279", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145810279#frequency_tab" }, { "id": "rs145810279", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145810279" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DFC->NFC).", "chr_id": "5", "chr_pos": "34911684", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D146", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "O60671-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O60671-1.155.155", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O60671-1.156.156", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60671-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1382257874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382257874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1382257874", "url": "https://www.ensembl.org/id/rs1382257874", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KINTQEPEETLDFDFCSTNV", "down_seq": "NKIILQSEGLREAFSELDMT", "snv": [ { "evidence": [ { "id": "rs1382257874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382257874" }, { "id": "rs1382257874", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1382257874" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVI->NVS).", "chr_id": "5", "chr_pos": "34911662", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I153", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1382257874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382257874" }, { "id": "rs1382257874", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1382257874" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVI->NVT).", "chr_id": "5", "chr_pos": "34911662", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I153", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O60671-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O60671-1.155.155", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O60671-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O60671-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O60671-1.173.173", "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": 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": "O60671-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762520471", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762520471", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762520471", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762520471", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762520471", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762520471#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762520471", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762520471", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TQEPEETLDFDFCSTNVINK", "down_seq": "ILQSEGLREAFSELDMTSEV", "snv": [ { "evidence": [ { "id": "rs762520471", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762520471" }, { "id": "rs762520471", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762520471" }, { "id": "rs762520471", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762520471#frequency_tab" }, { "id": "rs762520471", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762520471" } ], "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": "34911653", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I156", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O60671-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O60671-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O60671-1.155.155", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O60671-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O60671-1.173.173", "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": "O60671-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60671", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1248350352", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248350352", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1248350352", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1248350352#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1248350352", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1248350352", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NVINKIILQSEGLREAFSEL", "down_seq": "MTSEVLQITMSPDKPYFRLS", "snv": [ { "evidence": [ { "id": "O60671", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671" }, { "id": "rs1248350352", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248350352" }, { "id": "rs1248350352", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1248350352#frequency_tab" }, { "id": "rs1248350352", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1248350352" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DMT->NMT).", "chr_id": "5", "chr_pos": "34911609", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D171", "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": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O60671-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "O60671-1.155.155", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "O60671-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O60671-1.173.173", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60671-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60671", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "INKIILQSEGLREAFSELDM", "down_seq": "SEVLQITMSPDKPYFRLSTF", "snv": [ { "evidence": [ { "id": "O60671", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "34911602", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T173", "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": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O60671-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "O60671-1.155.155", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "O60671-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O60671-1.171.171", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60671-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1763744141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1763744141", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1763744141", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1763744141#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YPKDSDLMEAFHCNQTQVNR", "down_seq": "KISLLKPSTKALVLSCKVSI", "snv": [ { "evidence": [ { "id": "rs1763744141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1763744141" }, { "id": "rs1763744141", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1763744141#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRY->NRS).", "chr_id": "5", "chr_pos": "34908946", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y223", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O60671-1.226.233", "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": "O60671-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60671", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KPSTKALVLSCKVSIRTDNR", "down_seq": "FLSLQYMIRNEDGQICFVEY", "snv": [ { "evidence": [ { "id": "O60671", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRG->NRS).", "chr_id": "5", "chr_pos": "34908869", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G249", "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": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O60671-1.226.233", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O60671-1.244.244", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O60671-1.254.254", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O60671-1.256.256", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O60671-1.266.266", "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": "O60671-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1561170232", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1561170232", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1561170232", "url": "https://www.ensembl.org/id/rs1561170232", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TQQIQDEDDQYSLVASLDNV", "down_seq": "NLSTILKAIHFREHATCFAT", "snv": [ { "evidence": [ { "id": "rs1561170232", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1561170232" }, { "id": "rs1561170232", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1561170232" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVR->NVS).", "chr_id": "5", "chr_pos": "34914818", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R25", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O60671-1.26.26", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O60671-1.28.28", "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": "O60671-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60671", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DGQICFVEYYCCPDEEVPES", "down_seq": "", "snv": [ { "evidence": [ { "id": "O60671", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "34908772", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E281", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O60671-1.266.266", "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": "O60671-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs930669788", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs930669788", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs930669788", "url": "https://www.ncbi.nlm.nih.gov/snp/rs930669788#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs930669788", "url": "http://gnomad.broadinstitute.org/awesome?query=rs930669788", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IQDEDDQYSLVASLDNVRNL", "down_seq": "TILKAIHFREHATCFATKNG", "snv": [ { "evidence": [ { "id": "rs930669788", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs930669788" }, { "id": "rs930669788", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs930669788#frequency_tab" }, { "id": "rs930669788", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs930669788" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->NLF).", "chr_id": "5", "chr_pos": "34914810", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S28", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O60671-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O60671-1.26.26", "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": "O60671-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60671", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AFIQAGIFQEFKVQEESVTF", "down_seq": "INLTVLLDCLSIFGSSPMPG", "snv": [ { "evidence": [ { "id": "O60671", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "5", "chr_pos": "34913530", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R83", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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" ] }, { "evidence": [ { "id": "O60671", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671" } ], "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": "5", "chr_pos": "34913529", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R83", "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": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O60671-1.64.64", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O60671-1.85.85", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O60671-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O60671-1.98.98", "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": 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": "O60671-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750014454", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750014454", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750014454", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750014454", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750014454", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750014454", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AGIFQEFKVQEESVTFRINL", "down_seq": "VLLDCLSIFGSSPMPGTLTA", "snv": [ { "evidence": [ { "id": "rs750014454", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750014454" }, { "id": "rs750014454", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750014454" }, { "id": "rs750014454", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750014454" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLP).", "chr_id": "5", "chr_pos": "34913518", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T87", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O60671-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O60671-1.85.85", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O60671-1.98.98", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60671-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "O60671-1", "length": 282, "uniprot_id": "RAD1_HUMAN", "protein_name": "Cell cycle checkpoint protein RAD1", "refseq_ac": "NP_002844", "refseq_name": "cell cycle checkpoint protein RAD1", "gene_name": "RAD1", "gene_names_uniprotkb": "RAD1; REC1", "gene_names_refseq": "HRAD1; RAD1; REC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60671", "url": "https://www.uniprot.org/uniprotkb/O60671" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60671", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ESVTFRINLTVLLDCLSIFG", "down_seq": "SPMPGTLTALRMCYQGYGYP", "snv": [ { "evidence": [ { "id": "O60671", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60671" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "34913484", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S98", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "226", "end_pos": "233" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O60671-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "O60671-1.85.85", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O60671-1.87.87", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "O75832-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O75832-1", "length": 226, "uniprot_id": "PSD10_HUMAN", "protein_name": "26S proteasome non-ATPase regulatory subunit 10", "refseq_ac": "NP_002805", "refseq_name": "26S proteasome non-ATPase regulatory subunit 10 isoform 1", "gene_name": "PSMD10", "gene_names_uniprotkb": "PSMD10", "gene_names_refseq": "PSMD10; dJ889N15.2; p28(GANK); p28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75832", "url": "https://www.uniprot.org/uniprotkb/O75832" } ], "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": "O75832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75832" } ], "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": "O75832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75832" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "Regulation of the proteasome by AMPK in endothelial cells: the role of O-GlcNAc transferase (OGT).", "journal": "PloS one", "date": "2012", "authors": "Xu J, Wang S, Viollet B, Zou MH", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75832" } ], "reference": [ { "type": "PubMed", "id": "22574218", "url": "https://glygen.org/publication/PubMed/22574218" } ] } ], "crossref": [ { "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75832", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22574218", "url": "https://glygen.org/publication/PubMed/22574218", "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": "O75832", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75832" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "22574218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22574218" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "182", "end_pos": "182" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "199", "end_pos": "199" }, { "start_pos": "207", "end_pos": "207" } ] } ], "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": "O75832-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "O75832-1", "length": 226, "uniprot_id": "PSD10_HUMAN", "protein_name": "26S proteasome non-ATPase regulatory subunit 10", "refseq_ac": "NP_002805", "refseq_name": "26S proteasome non-ATPase regulatory subunit 10 isoform 1", "gene_name": "PSMD10", "gene_names_uniprotkb": "PSMD10", "gene_names_refseq": "PSMD10; dJ889N15.2; p28(GANK); p28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75832", "url": "https://www.uniprot.org/uniprotkb/O75832" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Reduced stability of retinoblastoma protein by gankyrin, an oncogenic ankyrin-repeat protein overexpressed in hepatomas.", "journal": "Nature medicine", "date": "2000", "authors": "Higashitsuji H, Itoh K, Nagao T, Dawson S, Nonoguchi K, Kido T, Mayer RJ, Arii S, Fujita J", "evidence": [ { "database": "UniProtKB", "id": "O75832", "url": "https://www.uniprot.org/uniprotkb/O75832" } ], "reference": [ { "type": "PubMed", "id": "10613832", "url": "https://glygen.org/publication/PubMed/10613832" } ] } ], "crossref": [ { "id": "O75832", "url": "https://www.uniprot.org/uniprotkb/O75832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10613832", "url": "https://glygen.org/publication/PubMed/10613832", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KASTNIQDTEGNTPLHLACD", "down_seq": "ERVEEAKLLVSQGASIYIEN", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Abolishes interaction with RB1.", "evidence": [ { "database": "UniProtKB", "id": "O75832", "url": "https://www.uniprot.org/uniprotkb/O75832" }, { "database": "PubMed", "id": "10613832", "url": "https://glygen.org/publication/PubMed/10613832" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "182", "end_pos": "182" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "199", "end_pos": "199" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "O75832-1.199.199", "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": "O75832-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "O75832-1", "length": 226, "uniprot_id": "PSD10_HUMAN", "protein_name": "26S proteasome non-ATPase regulatory subunit 10", "refseq_ac": "NP_002805", "refseq_name": "26S proteasome non-ATPase regulatory subunit 10 isoform 1", "gene_name": "PSMD10", "gene_names_uniprotkb": "PSMD10", "gene_names_refseq": "PSMD10; dJ889N15.2; p28(GANK); p28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75832", "url": "https://www.uniprot.org/uniprotkb/O75832" } ], "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": "O75832-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75832-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "O75832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ACDEERVEEAKLLVSQGASI", "down_seq": "IENKEEKTPLQVAKGGLGLI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75832" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Tyr199" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "182", "end_pos": "182" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "199", "end_pos": "199" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O75832-1.182.182", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O75832-1.207.207", "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": "O75832-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "O75832-1", "length": 226, "uniprot_id": "PSD10_HUMAN", "protein_name": "26S proteasome non-ATPase regulatory subunit 10", "refseq_ac": "NP_002805", "refseq_name": "26S proteasome non-ATPase regulatory subunit 10 isoform 1", "gene_name": "PSMD10", "gene_names_uniprotkb": "PSMD10", "gene_names_refseq": "PSMD10; dJ889N15.2; p28(GANK); p28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75832", "url": "https://www.uniprot.org/uniprotkb/O75832" } ], "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": "O75832-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75832-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O75832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75832", "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": "EAKLLVSQGASIYIENKEEK", "down_seq": "PLQVAKGGLGLILKRMVEG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75832" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr207" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "182", "end_pos": "182" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "199", "end_pos": "199" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O75832-1.199.199", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7L0Q8-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ARHGAP30 is a Wrch-1-interacting protein involved in actin dynamics and cell adhesion.", "journal": "Biochemical and biophysical research communications", "date": "2011", "authors": "Naji L, Pacholsky D, Aspenstrom P", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" } ] }, { "title": "Wrch-1, a novel member of the Rho gene family that is regulated by Wnt-1.", "journal": "Genes & development", "date": "2001", "authors": "Tao W, Pennica D, Xu L, Kalejta RF, Levine AJ", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "11459829", "url": "https://glygen.org/publication/PubMed/11459829" } ] }, { "title": "Identification of a bipartite focal adhesion localization signal in RhoU/Wrch-1, a Rho family GTPase that regulates cell adhesion and migration.", "journal": "Biology of the cell", "date": "2007", "authors": "Ory S, Brazier H, Blangy A", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11459829", "url": "https://glygen.org/publication/PubMed/11459829", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SAVVSVDGRPVRLQLCDTAG", "down_seq": "DEFDKLRPLCYTNTDIFLLC", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "L", "comment": "Constitutively active. Results in increased rates of stress fiber dissolution and cell migration. No effect on ARHGAP30-binding.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" }, { "database": "PubMed", "id": "11459829", "url": "https://glygen.org/publication/PubMed/11459829" }, { "database": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q7L0Q8-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7L0Q8-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PAK4 promotes kinase-independent stabilization of RhoU to modulate cell adhesion.", "journal": "The Journal of cell biology", "date": "2015", "authors": "Dart AE, Box GM, Court W, Gale ME, Brown JP, Pinder SE, Eccles SA, Wells CM", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "26598620", "url": "https://glygen.org/publication/PubMed/26598620" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26598620", "url": "https://glygen.org/publication/PubMed/26598620", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ILVGTQSDLREDVKVLIELD", "down_seq": "CKEKPVPEEAAKLCAEEIKA", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Decreased ubiquitination.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "26598620", "url": "https://glygen.org/publication/PubMed/26598620" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "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": "Q7L0Q8-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PAK4 promotes kinase-independent stabilization of RhoU to modulate cell adhesion.", "journal": "The Journal of cell biology", "date": "2015", "authors": "Dart AE, Box GM, Court W, Gale ME, Brown JP, Pinder SE, Eccles SA, Wells CM", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "26598620", "url": "https://glygen.org/publication/PubMed/26598620" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26598620", "url": "https://glygen.org/publication/PubMed/26598620", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TQQQPKKSKSRTPDKMKNLS", "down_seq": "SWWKKYCCFV", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Decreased ubiquitination.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "26598620", "url": "https://glygen.org/publication/PubMed/26598620" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q7L0Q8-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7L0Q8-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7L0Q8-1.255.255", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7L0Q8-1.256.256", "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": "Q7L0Q8-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Transforming activity of the Rho family GTPase, Wrch-1, a Wnt-regulated Cdc42 homolog, is dependent on a novel carboxyl-terminal palmitoylation motif.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Berzat AC, Buss JE, Chenette EJ, Weinbaum CA, Shutes A, Der CJ, Minden A, Cox AD", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "16046391", "url": "https://glygen.org/publication/PubMed/16046391" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16046391", "url": "https://glygen.org/publication/PubMed/16046391", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "SKSRTPDKMKNLSKSWWKKY", "down_seq": "CFV", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "No effect on subcellular location.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "16046391", "url": "https://glygen.org/publication/PubMed/16046391" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q7L0Q8-1.248.248", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q7L0Q8-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7L0Q8-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7L0Q8-1.256.256", "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": "Q7L0Q8-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Transforming activity of the Rho family GTPase, Wrch-1, a Wnt-regulated Cdc42 homolog, is dependent on a novel carboxyl-terminal palmitoylation motif.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Berzat AC, Buss JE, Chenette EJ, Weinbaum CA, Shutes A, Der CJ, Minden A, Cox AD", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "16046391", "url": "https://glygen.org/publication/PubMed/16046391" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16046391", "url": "https://glygen.org/publication/PubMed/16046391", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "KSRTPDKMKNLSKSWWKKYC", "down_seq": "FV", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "Loss of subcellular location to plasma and intracellular membranes.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "16046391", "url": "https://glygen.org/publication/PubMed/16046391" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q7L0Q8-1.248.248", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7L0Q8-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7L0Q8-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7L0Q8-1.255.255", "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": "Q7L0Q8-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ARHGAP30 is a Wrch-1-interacting protein involved in actin dynamics and cell adhesion.", "journal": "Biochemical and biophysical research communications", "date": "2011", "authors": "Naji L, Pacholsky D, Aspenstrom P", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" } ] }, { "title": "Wrch-1, a novel member of the Rho gene family that is regulated by Wnt-1.", "journal": "Genes & development", "date": "2001", "authors": "Tao W, Pennica D, Xu L, Kalejta RF, Levine AJ", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "11459829", "url": "https://glygen.org/publication/PubMed/11459829" } ] }, { "title": "Identification of a bipartite focal adhesion localization signal in RhoU/Wrch-1, a Rho family GTPase that regulates cell adhesion and migration.", "journal": "Biology of the cell", "date": "2007", "authors": "Ory S, Brazier H, Blangy A", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11459829", "url": "https://glygen.org/publication/PubMed/11459829", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GGAEGRGVKCVLVGDGAVGK", "down_seq": "SLVVSYTTNGYPTEYIPTAF", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "N", "comment": "Loss of GTP-binding and localization to focal adhesions. No effect on ARHGAP30-binding.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" }, { "database": "PubMed", "id": "11459829", "url": "https://glygen.org/publication/PubMed/11459829" }, { "database": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q7L0Q8-1.80.80", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q7L0Q8-1.81.81", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q7L0Q8-1.83.83", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7L0Q8-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ARHGAP30 is a Wrch-1-interacting protein involved in actin dynamics and cell adhesion.", "journal": "Biochemical and biophysical research communications", "date": "2011", "authors": "Naji L, Pacholsky D, Aspenstrom P", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VGKTSLVVSYTTNGYPTEYI", "down_seq": "TAFDNFSAVVSVDGRPVRLQ", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "G", "comment": "No effect on ARHGAP30-binding.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q7L0Q8-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7L0Q8-1.81.81", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7L0Q8-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7L0Q8-1.86.86", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7L0Q8-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7L0Q8-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of a bipartite focal adhesion localization signal in RhoU/Wrch-1, a Rho family GTPase that regulates cell adhesion and migration.", "journal": "Biology of the cell", "date": "2007", "authors": "Ory S, Brazier H, Blangy A", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GKTSLVVSYTTNGYPTEYIP", "down_seq": "AFDNFSAVVSVDGRPVRLQL", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "S", "comment": "Loss of binding to PAK3; when associated with A-83 and C-86.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q7L0Q8-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7L0Q8-1.80.80", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7L0Q8-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7L0Q8-1.86.86", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q7L0Q8-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7L0Q8-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ARHGAP30 is a Wrch-1-interacting protein involved in actin dynamics and cell adhesion.", "journal": "Biochemical and biophysical research communications", "date": "2011", "authors": "Naji L, Pacholsky D, Aspenstrom P", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" } ] }, { "title": "Identification of a bipartite focal adhesion localization signal in RhoU/Wrch-1, a Rho family GTPase that regulates cell adhesion and migration.", "journal": "Biology of the cell", "date": "2007", "authors": "Ory S, Brazier H, Blangy A", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "TSLVVSYTTNGYPTEYIPTA", "down_seq": "DNFSAVVSVDGRPVRLQLCD", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Loss of binding to PAK3; when associated with S-81 and C-86.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" }, { "database": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] }, { "sequence_org": "F", "sequence_mut": "G", "comment": "Loss of ARHGAP30-binding.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" }, { "database": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q7L0Q8-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7L0Q8-1.80.80", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7L0Q8-1.81.81", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7L0Q8-1.86.86", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7L0Q8-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7L0Q8-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ARHGAP30 is a Wrch-1-interacting protein involved in actin dynamics and cell adhesion.", "journal": "Biochemical and biophysical research communications", "date": "2011", "authors": "Naji L, Pacholsky D, Aspenstrom P", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" } ], "reference": [ { "type": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" } ] }, { "title": "Identification of a bipartite focal adhesion localization signal in RhoU/Wrch-1, a Rho family GTPase that regulates cell adhesion and migration.", "journal": "Biology of the cell", "date": "2007", "authors": "Ory S, Brazier H, Blangy A", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VVSYTTNGYPTEYIPTAFDN", "down_seq": "SAVVSVDGRPVRLQLCDTAG", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "C", "comment": "Loss of PAK3-binding; when associated with S-81 and A-83. No effect on ARHGAP30-binding.", "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" }, { "database": "PubMed", "id": "21565175", "url": "https://glygen.org/publication/PubMed/21565175" }, { "database": "PubMed", "id": "17620058", "url": "https://glygen.org/publication/PubMed/17620058" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q7L0Q8-1.80.80", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7L0Q8-1.81.81", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7L0Q8-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7L0Q8-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7L0Q8-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7L0Q8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7L0Q8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQQPKKSKSRTPDKMKNLSK", "down_seq": "WWKKYCCFV", "snv": [ { "evidence": [ { "id": "Q7L0Q8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7L0Q8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "1", "chr_pos": "228743709", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S249", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q7L0Q8-1.248.248", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7L0Q8-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7L0Q8-1.255.255", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7L0Q8-1.256.256", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7L0Q8-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7L0Q8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7L0Q8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EYIPTAFDNFSAVVSVDGRP", "down_seq": "RLQLCDTAGQDEFDKLRPLC", "snv": [ { "evidence": [ { "id": "Q7L0Q8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7L0Q8" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "228737699", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V97", "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: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": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q7L0Q8-1.80.80", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q7L0Q8-1.81.81", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q7L0Q8-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q7L0Q8-1.86.86", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7L0Q8-1.107.107", "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": "Q7L0Q8-1.254.254", "start_pos": 254, "end_pos": 254, "uniprot_canonical_ac": "Q7L0Q8-1", "length": 258, "uniprot_id": "RHOU_HUMAN", "protein_name": "Rho-related GTP-binding protein RhoU", "refseq_ac": "NP_067028", "refseq_name": "rho-related GTP-binding protein RhoU", "gene_name": "RHOU", "gene_names_uniprotkb": "RHOU; ARHU; CDC42L1; G28K; SB128; WRCH1", "gene_names_refseq": "ARHU; CDC42L1; G28K; RHOU; WRCH1; hG28K", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7L0Q8", "url": "https://www.uniprot.org/uniprotkb/Q7L0Q8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Regulation of the Rho family small GTPase Wrch-1/RhoU by C-terminal tyrosine phosphorylation requires Src.", "journal": "Molecular and cellular biology", "date": "2010", "authors": "Alan JK, Berzat AC, Dewar BJ, Graves LM, Cox AD", "evidence": [ { "database": "Reactome", "id": "R-HSA-9013420", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9013420" }, { "database": "iPTMnet", "id": "Q7L0Q8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7L0Q8" } ], "reference": [ { "type": "PubMed", "id": "20547754", "url": "https://glygen.org/publication/PubMed/20547754" } ] } ], "crossref": [ { "id": "Q7L0Q8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7L0Q8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20547754", "url": "https://glygen.org/publication/PubMed/20547754", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KSKSRTPDKMKNLSKSWWKK", "down_seq": "CCFV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7L0Q8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7L0Q8" }, { "database": "PubMed", "id": "20547754", "url": "https://glygen.org/publication/PubMed/20547754" } ], "site_lbl": "Tyr254" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7L0Q8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7L0Q8" }, { "database": "PubMed", "id": "20547754", "url": "https://glygen.org/publication/PubMed/20547754" } ], "site_lbl": "Tyr254" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "86", "end_pos": "86" } ] }, { "type": "snv", "site_list": [ { "start_pos": "249", "end_pos": "249" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "254", "end_pos": "254" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q7L0Q8-1.248.248", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7L0Q8-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7L0Q8-1.255.255", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7L0Q8-1.256.256", "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": 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": "Q9NWF9-2.664.664", "start_pos": 664, "end_pos": 664, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.", "journal": "Molecular cell", "date": "2022", "authors": "Cotton TR, Cobbold SA, Bernardini JP, Richardson LW, Wang XS, Lechtenberg BC", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "RefSeq", "id": "NP_996994", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_996994" }, { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" } ], "reference": [ { "type": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "crossref": [ { "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "NGLTCEELAEKDDIKYRTSI", "down_seq": "EKMTAARIRKCHKCGTGLIK", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Abrogates ubiquitin chain formation activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9NWF9-2.672.672", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9NWF9-2.683.683", "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": "Q9NWF9-2.672.672", "start_pos": 672, "end_pos": 672, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.", "journal": "Molecular cell", "date": "2022", "authors": "Cotton TR, Cobbold SA, Bernardini JP, Richardson LW, Wang XS, Lechtenberg BC", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "RefSeq", "id": "NP_996994", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_996994" }, { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" } ], "reference": [ { "type": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "crossref": [ { "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "AEKDDIKYRTSIEEKMTAAR", "down_seq": "RKCHKCGTGLIKSEGCNRMS", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "A", "comment": "Abrogates ubiquitin chain formation activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9NWF9-2.664.664", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9NWF9-2.683.683", "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": "Q9NWF9-2.683.683", "start_pos": 683, "end_pos": 683, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.", "journal": "Molecular cell", "date": "2022", "authors": "Cotton TR, Cobbold SA, Bernardini JP, Richardson LW, Wang XS, Lechtenberg BC", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "RefSeq", "id": "NP_996994", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_996994" }, { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" } ], "reference": [ { "type": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "crossref": [ { "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "IEEKMTAARIRKCHKCGTGL", "down_seq": "KSEGCNRMSCRCGAQMCYLC", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "A", "comment": "Abrogates ubiquitin chain formation activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9NWF9-2.664.664", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9NWF9-2.672.672", "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": "Q9NWF9-2.719.719", "start_pos": 719, "end_pos": 719, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.", "journal": "Molecular cell", "date": "2022", "authors": "Cotton TR, Cobbold SA, Bernardini JP, Richardson LW, Wang XS, Lechtenberg BC", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "RefSeq", "id": "NP_996994", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_996994" }, { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" } ], "reference": [ { "type": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "crossref": [ { "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MCYLCRVSINGYDHFCQHPR", "down_seq": "PGAPCQECSRCSLWTDPTED", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Mild reduced activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MAPK1", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" }, { "database": "PubMed", "id": "34998453", "url": "https://glygen.org/publication/PubMed/34998453" } ], "site_lbl": "Ser719" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9NWF9-2.469.469", "start_pos": 469, "end_pos": 469, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NWF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NWF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IEKRMFFLENKRRHCRSYDR", "down_seq": "ALLPAVQQEQEFYEQKIKEM", "snv": [ { "evidence": [ { "id": "Q9NWF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NWF9" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "5721100", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R469", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "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": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NWF9-2.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NWF9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NWF9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DSSDEERIPMLVTPAPQQHE", "down_seq": "EDLDDDVILTEDDSEDDYGE", "snv": [ { "evidence": [ { "id": "Q9NWF9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NWF9" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "5752881", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E56", "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": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NWF9-2.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q9NWF9-2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9-2" } ], "reference": [ { "type": "PubMed", "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679" } ] } ], "crossref": [ { "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NFHCHRGQEWINLRDGPITI", "down_seq": "DSSDEERIPMLVTPAPQQHE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" }, { "database": "PubMed", "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679" } ], "site_lbl": "Ser35" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "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": "Q9NWF9-2.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "Q9NWF9-2", "length": 866, "uniprot_id": "RN216_HUMAN", "protein_name": "E3 ubiquitin-protein ligase RNF216", "refseq_ac": "NP_996994", "refseq_name": "E3 ubiquitin-protein ligase RNF216 isoform a", "gene_name": "RNF216", "gene_names_uniprotkb": "RNF216; TRIAD3; UBCE7IP1; ZIN", "gene_names_refseq": "CAHH; RNF216; TRIAD3; U7I1; UBCE7IP1; ZIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" } ], "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": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q9NWF9-2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9-2" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9", "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": "GHYAITRKALSDAIKKWQEL", "down_seq": "PETSGKRKKRKQMNQYSYID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9NWF9", "url": "https://www.uniprot.org/uniprotkb/Q9NWF9" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9NWF9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NWF9" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser419" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "664", "end_pos": "664" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "719", "end_pos": "719" } ] }, { "type": "snv", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "56", "end_pos": "56" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "719", "end_pos": "719" } ] } ], "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": "Q13404-4.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q13404-4", "length": 147, "uniprot_id": "UB2V1_HUMAN", "protein_name": "Ubiquitin-conjugating enzyme E2 variant 1", "refseq_ac": "NP_001027459", "refseq_name": "ubiquitin-conjugating enzyme E2 variant 1 isoform d", "gene_name": "UBE2V1", "gene_names_uniprotkb": "UBE2V1; CROC1; OKcl.19; UBE2V; UEV1", "gene_names_refseq": "CIR1; CROC-1; CROC1; UBE2V1; UBE2V; UEV-1; UEV1A; UEV1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13404", "url": "https://www.uniprot.org/uniprotkb/Q13404" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Multi-comparative Thermal Proteome Profiling Uncovers New O-GlcNAc Proteins in a System-wide Method.", "journal": "Analytical chemistry", "date": "2022-12-29", "authors": "Wang Guoli, Li Yang, Wang Ting, Wang Jun, Yao Jun, Yan Guoquan, Zhang Ying, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q13404", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404" } ], "reference": [ { "type": "PubMed", "id": "36580660", "url": "https://glygen.org/publication/PubMed/36580660" } ] }, { "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": "Q13404", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q13404", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404" } ], "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": "Q13404", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404" } ], "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": "Q13404", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404" } ], "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": "Q13404", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "36580660", "url": "https://glygen.org/publication/PubMed/36580660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13404", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "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": "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": "36580660", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36580660" }, { "id": "Q13404", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13404" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "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": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] } ], "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13404-4.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q13404-4", "length": 147, "uniprot_id": "UB2V1_HUMAN", "protein_name": "Ubiquitin-conjugating enzyme E2 variant 1", "refseq_ac": "NP_001027459", "refseq_name": "ubiquitin-conjugating enzyme E2 variant 1 isoform d", "gene_name": "UBE2V1", "gene_names_uniprotkb": "UBE2V1; CROC1; OKcl.19; UBE2V; UEV1", "gene_names_refseq": "CIR1; CROC-1; CROC1; UBE2V1; UBE2V; UEV-1; UEV1A; UEV1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13404", "url": "https://www.uniprot.org/uniprotkb/Q13404" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13404", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13404", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSSNGVVDPRAISVLAKWQN", "down_seq": "YSIKVVLQELRRLMMSKENM", "snv": [ { "evidence": [ { "id": "Q13404", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13404" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "50082871", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S114", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" } ] }, { "type": "phosphorylation", "site_list": [ { "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": "Q13404-4.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "Q13404-4", "length": 147, "uniprot_id": "UB2V1_HUMAN", "protein_name": "Ubiquitin-conjugating enzyme E2 variant 1", "refseq_ac": "NP_001027459", "refseq_name": "ubiquitin-conjugating enzyme E2 variant 1 isoform d", "gene_name": "UBE2V1", "gene_names_uniprotkb": "UBE2V1; CROC1; OKcl.19; UBE2V; UEV1", "gene_names_refseq": "CIR1; CROC-1; CROC1; UBE2V1; UBE2V; UEV-1; UEV1A; UEV1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13404", "url": "https://www.uniprot.org/uniprotkb/Q13404" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "journal": "Proteomics", "date": "2008", "authors": "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "evidence": [ { "database": "iPTMnet", "id": "Q13404-4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13404-4" } ], "reference": [ { "type": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" } ] } ], "crossref": [ { "id": "Q13404", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13404", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SLKIECGPKYPEAPPFVRFV", "down_seq": "KINMNGVNSSNGVVDPRAIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13404", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13404" }, { "database": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" } ], "site_lbl": "Thr86" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] } ], "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": "Q9BQS7-1.1066.1077", "start_pos": 1066, "end_pos": 1077, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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": "TEHLSPLTVITK", "start_aa": "T", "up_seq": "CHVTDHVHAGMETLFTVFSR", "down_seq": "ETEKAVPPRDIEEGNVKMLG", "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": "TEHLSPLTVITK", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Lys", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9BQS7-1.1066.1081", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BQS7-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BQS7-1.1073.1073", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BQS7-1.1076.1076", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.1079.1079", "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" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 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": "Q9BQS7-1.1066.1081", "start_pos": 1066, "end_pos": 1081, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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": "TEHLSPLTVITKETEK", "start_aa": "T", "up_seq": "CHVTDHVHAGMETLFTVFSR", "down_seq": "AVPPRDIEEGNVKMLGMQIP", "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": "TEHLSPLTVITKETEK", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Lys", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9BQS7-1.1066.1077", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BQS7-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.1073.1073", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.1076.1076", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.1079.1079", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BQS7-1.1098.1098", "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": "Q9BQS7-1.1070.1070", "start_pos": 1070, "end_pos": 1070, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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" } ] }, { "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": "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": "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DHVHAGMETLFTVFSRTEHL", "down_seq": "PLTVITKETEKAVPPRDIEE", "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": "Ser1070", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9BQS7-1.1066.1077", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BQS7-1.1066.1081", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BQS7-1.1073.1073", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BQS7-1.1076.1076", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BQS7-1.1079.1079", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BQS7-1.1073.1073", "start_pos": 1073, "end_pos": 1073, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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" } ] }, { "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": "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": "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": "rs1427436172", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427436172", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1427436172", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427436172", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HAGMETLFTVFSRTEHLSPL", "down_seq": "VITKETEKAVPPRDIEEGNV", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1073", "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": "rs1427436172", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427436172" }, { "id": "rs1427436172", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427436172" } ], "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": "66263662", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1073", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9BQS7-1.1066.1077", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.1066.1081", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BQS7-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BQS7-1.1076.1076", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BQS7-1.1079.1079", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BQS7-1.1076.1076", "start_pos": 1076, "end_pos": 1076, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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" } ] }, { "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": "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": "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" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "METLFTVFSRTEHLSPLTVI", "down_seq": "KETEKAVPPRDIEEGNVKML", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1076", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9BQS7-1.1066.1077", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.1066.1081", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BQS7-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BQS7-1.1073.1073", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BQS7-1.1079.1079", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BQS7-1.1079.1079", "start_pos": 1079, "end_pos": 1079, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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": "T", "start_aa": "T", "up_seq": "LFTVFSRTEHLSPLTVITKE", "down_seq": "EKAVPPRDIEEGNVKMLGMQ", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1079", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.1066.1077", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.1066.1081", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BQS7-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BQS7-1.1073.1073", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BQS7-1.1076.1076", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BQS7-1.1098.1098", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BQS7-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GSSGPLKADDSVPPGGSHIY", "down_seq": "WTIPEGHAPTDADPACLTWI", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn164", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PPQRQDVDHDFFLLFSVVDE", "down_seq": "LSWHLNENIATYCSDPASVD", "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": "Asn236", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQS7-1.246.246", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.588.588", "start_pos": 588, "end_pos": 588, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1417395794", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1417395794", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1417395794", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1417395794", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DGKQKGVDKEFFLLFTVLDE", "down_seq": "KSWYSNANQAAAMLDFRLLS", "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": "Asn588", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1417395794", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1417395794" }, { "id": "rs1417395794", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1417395794" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKS->SKS).", "chr_id": "X", "chr_pos": "66198927", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N588", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.590.590", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQS7-1.598.598", "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": "Q9BQS7-1.714.714", "start_pos": 714, "end_pos": 714, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2088581937", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088581937", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2088581937", "url": "https://www.ensembl.org/id/rs2088581937", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TFEIYCQAGSHREAGMRAIY", "down_seq": "VSQCPGHQATPRQRYQAARI", "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": "Asn714", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2088581937", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088581937" }, { "id": "rs2088581937", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2088581937" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->YVS).", "chr_id": "X", "chr_pos": "66203426", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N714", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.722.722", "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": 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": "Q9BQS7-1.758.758", "start_pos": 758, "end_pos": 758, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MAEEVEWDYCPDRSWEREWH", "down_seq": "QSEKDSYGYIFLSNKDGLLG", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "EWHnQSEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn758", "evidence": [ { "id": "37074911", "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": "EWHnQSEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn758", "evidence": [ { "id": "37074911", "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": "Asn758", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.760.760", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BQS7-1.762.762", "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": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BQS7-1.829.829", "start_pos": 829, "end_pos": 829, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ILGPLIKGEVGDILTVVFKN", "down_seq": "ASRPYSVHAHGVLESTTVWP", "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": "Asn829", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9BQS7-1.830.830", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BQS7-1.844.844", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.873.873", "start_pos": 873, "end_pos": 873, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1170673873", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170673873", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1170673873", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1170673873#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61741152", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61741152", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61741152", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61741152", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61741152", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61741152", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61741152", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61741152#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61741152", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61741152", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EPGEVVTYQWNIPERSGPGP", "down_seq": "DSACVSWIYYSAVDPIKDMY", "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": "Asn873", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1170673873", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170673873" }, { "id": "rs1170673873", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1170673873#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDS->KDS).", "chr_id": "X", "chr_pos": "66255090", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N873", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs61741152", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61741152" }, { "id": "rs61741152", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61741152" }, { "id": "rs61741152", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61741152" }, { "id": "rs61741152", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61741152#frequency_tab" }, { "id": "rs61741152", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61741152" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDS->SDS).", "chr_id": "X", "chr_pos": "66255089", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N873", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.865.865", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.931.931", "start_pos": 931, "end_pos": 931, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HGGRSDMDREFALLFLIFDE", "down_seq": "KSWYLEENVATHGSQDPGSI", "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": "Asn931", "evidence": [ { "id": "Q9BQS7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.933.933", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQS7-1.941.941", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BQS7-1.943.943", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Functional role of the putative iron ligands in the ferroxidase activity of recombinant human hephaestin.", "journal": "Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry", "date": "2012-12", "authors": "Vashchenko Ganna, Macgillivray Ross T A", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "NIATYCSDPASVDKEDETFQ", "down_seq": "SNRMHAINGFVFGNLPELNM", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Decreased affinity for Fe(2+) and decreased ferroxidase activity; when associated with A-269, A-616 and A-621. Loss of affinity for Fe(2+) and loss of ferroxidase activity; when associated with A-269, A-960 and A-965.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BQS7-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9BQS7-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.269.269", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BQS7-1.280.280", "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": "Q9BQS7-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Functional role of the putative iron ligands in the ferroxidase activity of recombinant human hephaestin.", "journal": "Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry", "date": "2012-12", "authors": "Vashchenko Ganna, Macgillivray Ross T A", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "CSDPASVDKEDETFQESNRM", "down_seq": "AINGFVFGNLPELNMCAQKR", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Decreased affinity for Fe(2+) and decreased ferroxidase activity; when associated with A-264, A-616 and A-621. Loss of affinity for Fe(2+) and loss of ferroxidase activity; when associated with A-264, A-960 and A-965.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BQS7-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.264.264", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BQS7-1.280.280", "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": "Q9BQS7-1.616.616", "start_pos": 616, "end_pos": 616, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Functional role of the putative iron ligands in the ferroxidase activity of recombinant human hephaestin.", "journal": "Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry", "date": "2012-12", "authors": "Vashchenko Ganna, Macgillivray Ross T A", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NQAAAMLDFRLLSEDIEGFQ", "down_seq": "SNRMHAINGFLFSNLPRLDM", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Decreased affinity for Fe(2+) and decreased ferroxidase activity; when associated with A-264, A-269 and A-621.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BQS7-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9BQS7-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.621.621", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BQS7-1.632.632", "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": "Q9BQS7-1.621.621", "start_pos": 621, "end_pos": 621, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Functional role of the putative iron ligands in the ferroxidase activity of recombinant human hephaestin.", "journal": "Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry", "date": "2012-12", "authors": "Vashchenko Ganna, Macgillivray Ross T A", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "MLDFRLLSEDIEGFQDSNRM", "down_seq": "AINGFLFSNLPRLDMCKGDT", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Decreased affinity for Fe(2+) and decreased ferroxidase activity; when associated with A-264, A-269 and A-616.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.616.616", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BQS7-1.632.632", "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": "Q9BQS7-1.960.960", "start_pos": 960, "end_pos": 960, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Functional role of the putative iron ligands in the ferroxidase activity of recombinant human hephaestin.", "journal": "Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry", "date": "2012-12", "authors": "Vashchenko Ganna, Macgillivray Ross T A", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VATHGSQDPGSINLQDETFL", "down_seq": "SNKMHAINGKLYANLRGLTM", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Loss of affinity for Fe(2+) and loss of ferroxidase activity; when associated with A-264, A-269 and A-965.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9BQS7-1.941.941", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9BQS7-1.943.943", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.965.965", "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": "Q9BQS7-1.965.965", "start_pos": 965, "end_pos": 965, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Functional role of the putative iron ligands in the ferroxidase activity of recombinant human hephaestin.", "journal": "Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry", "date": "2012-12", "authors": "Vashchenko Ganna, Macgillivray Ross T A", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SQDPGSINLQDETFLESNKM", "down_seq": "AINGKLYANLRGLTMYQGER", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Loss of affinity for Fe(2+) and loss of ferroxidase activity; when associated with A-264, A-269 and A-960.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "22961397", "url": "https://glygen.org/publication/PubMed/22961397" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.960.960", "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": "Q9BQS7-1.933.933", "start_pos": 933, "end_pos": 933, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GRSDMDREFALLFLIFDENK", "down_seq": "WYLEENVATHGSQDPGSINL", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "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 2 filters: num. of cancers (4); n-glyco-sequon-loss (NKS->NKF).", "chr_id": "23", "chr_pos": "66256232", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S933", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.931.931", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.941.941", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQS7-1.943.943", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.1098.1098", "start_pos": 1098, "end_pos": 1098, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "ETEKAVPPRDIEEGNVKMLG", "down_seq": "QIPIKNVEMLASVLVAISVT", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "66266489", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M1098", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BQS7-1.1066.1081", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9BQS7-1.1079.1079", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.1103.1103", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BQS7-1.1116.1116", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.1103.1103", "start_pos": 1103, "end_pos": 1103, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VPPRDIEEGNVKMLGMQIPI", "down_seq": "NVEMLASVLVAISVTLLLVV", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "66266504", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K1103", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.1098.1098", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BQS7-1.1116.1116", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.1116.1116", "start_pos": 1116, "end_pos": 1116, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs143252537", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143252537", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143252537", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143252537", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs143252537", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143252537", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143252537", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143252537#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143252537", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143252537", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGMQIPIKNVEMLASVLVAI", "down_seq": "VTLLLVVLALGGVVWYQHRQ", "snv": [ { "evidence": [ { "id": "rs143252537", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143252537" }, { "id": "rs143252537", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143252537" }, { "id": "rs143252537", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143252537" }, { "id": "rs143252537", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143252537#frequency_tab" }, { "id": "rs143252537", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143252537" } ], "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": "X", "chr_pos": "66266542", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1116", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BQS7-1.1098.1098", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9BQS7-1.1103.1103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.1140.1140", "start_pos": 1140, "end_pos": 1140, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLVVLALGGVVWYQHRQRKL", "down_seq": "RNRRSILDDSFKLLSFKQ", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "23", "chr_pos": "66266614", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1140", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.1145.1145", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQS7-1.1150.1150", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BQS7-1.1155.1155", "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": "Q9BQS7-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1387338595", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1387338595", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1387338595", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1387338595", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HLKNFATRPYTIHPHGVFYE", "down_seq": "DSEGSLYPDGSSGPLKADDS", "snv": [ { "evidence": [ { "id": "rs1387338595", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1387338595" }, { "id": "rs1387338595", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1387338595" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KDS->NDS).", "chr_id": "X", "chr_pos": "66172589", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K134", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1386603194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386603194", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1386603194", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386603194", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QRQDVDHDFFLLFSVVDENL", "down_seq": "WHLNENIATYCSDPASVDKE", "snv": [ { "evidence": [ { "id": "rs1386603194", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386603194" }, { "id": "rs1386603194", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386603194" } ], "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 (NLS->NLN).", "chr_id": "X", "chr_pos": "66188446", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S238", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.236.236", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BQS7-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.246.246", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756918779", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756918779", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756918779", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756918779", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756918779", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756918779", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HDFFLLFSVVDENLSWHLNE", "down_seq": "IATYCSDPASVDKEDETFQE", "snv": [ { "evidence": [ { "id": "rs756918779", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756918779" }, { "id": "rs756918779", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756918779" }, { "id": "rs756918779", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756918779" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEN->NES).", "chr_id": "X", "chr_pos": "66188464", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N244", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.236.236", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BQS7-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BQS7-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9BQS7-1.264.264", "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": "Q9BQS7-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781019310", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781019310", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781019310", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781019310", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781019310", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781019310", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FFLLFSVVDENLSWHLNENI", "down_seq": "TYCSDPASVDKEDETFQESN", "snv": [ { "evidence": [ { "id": "rs781019310", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781019310" }, { "id": "rs781019310", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781019310" }, { "id": "rs781019310", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781019310" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIA->NIS).", "chr_id": "X", "chr_pos": "66188469", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A246", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BQS7-1.236.236", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BQS7-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BQS7-1.264.264", "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": "Q9BQS7-1.259.259", "start_pos": 259, "end_pos": 259, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "WHLNENIATYCSDPASVDKE", "down_seq": "ETFQESNRMHAINGFVFGNL", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DET->NET).", "chr_id": "23", "chr_pos": "66188508", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D259", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9BQS7-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9BQS7-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.264.264", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQS7-1.269.269", "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": "Q9BQS7-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs767130933", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767130933", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767130933", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767130933", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767130933", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767130933", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs767130933", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs767130933", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ETFQESNRMHAINGFVFGNL", "down_seq": "ELNMCAQKRVAWHLFGMGNE", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" }, { "id": "rs767130933", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767130933" }, { "id": "rs767130933", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767130933" }, { "id": "rs767130933", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767130933" }, { "id": "rs767130933", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs767130933" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLP->NLT).", "chr_id": "23", "chr_pos": "66189713", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P280", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BQS7-1.264.264", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BQS7-1.269.269", "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": "Q9BQS7-1.407.407", "start_pos": 407, "end_pos": 407, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HEIQWDYGPMGHDGSTGKNL", "down_seq": "EPGSISDKFFQKSSSRIGGT", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "23", "chr_pos": "66192286", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R407", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q9BQS7-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BQS7-1.423.423", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q9BQS7-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1159481329", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159481329", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1159481329", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159481329#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSTGKNLREPGSISDKFFQK", "down_seq": "SSRIGGTYWKVRYEAFQDET", "snv": [ { "evidence": [ { "id": "rs1159481329", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159481329" }, { "id": "rs1159481329", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159481329#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "X", "chr_pos": "66193528", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S420", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9BQS7-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BQS7-1.423.423", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BQS7-1.432.432", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.423.423", "start_pos": 423, "end_pos": 423, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GKNLREPGSISDKFFQKSSS", "down_seq": "IGGTYWKVRYEAFQDETFQE", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "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": "23", "chr_pos": "66193537", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R423", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BQS7-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BQS7-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BQS7-1.432.432", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ISDKFFQKSSSRIGGTYWKV", "down_seq": "YEAFQDETFQEKMHLEEDRH", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "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": "23", "chr_pos": "66193563", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R432", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID: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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9BQS7-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BQS7-1.423.423", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.461.461", "start_pos": 461, "end_pos": 461, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FQEKMHLEEDRHLGILGPVI", "down_seq": "AEVGDTIQVVFYNRASQPFS", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "23", "chr_pos": "66192286", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R461", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q9BQS7-1.500.500", "start_pos": 500, "end_pos": 500, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FSMQPHGVFYEKDYEGTVYN", "down_seq": "GSSYPGLVAKPFEKVTYRWT", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DGS->NGS).", "chr_id": "23", "chr_pos": "66195226", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D500", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9BQS7-1.501.501", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.501.501", "start_pos": 501, "end_pos": 501, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147744626", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147744626", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147744626", "url": "https://www.ensembl.org/id/rs2147744626", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SMQPHGVFYEKDYEGTVYND", "down_seq": "SSYPGLVAKPFEKVTYRWTV", "snv": [ { "evidence": [ { "id": "rs2147744626", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147744626" }, { "id": "rs2147744626", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147744626" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDG->NDC).", "chr_id": "X", "chr_pos": "66195229", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G501", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9BQS7-1.500.500", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.552.552", "start_pos": 552, "end_pos": 552, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PACLTWMYFSAADPIRDTNS", "down_seq": "LVGPLLVCRAGALGADGKQK", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "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 (NSG->NSS).", "chr_id": "23", "chr_pos": "66197835", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G552", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.590.590", "start_pos": 590, "end_pos": 590, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747247245", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747247245", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747247245", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747247245", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747247245", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747247245", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KQKGVDKEFFLLFTVLDENK", "down_seq": "WYSNANQAAAMLDFRLLSED", "snv": [ { "evidence": [ { "id": "rs747247245", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747247245" }, { "id": "rs747247245", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747247245" }, { "id": "rs747247245", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747247245" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKS->NKG).", "chr_id": "X", "chr_pos": "66198932", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S590", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.588.588", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BQS7-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.598.598", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.596.596", "start_pos": 596, "end_pos": 596, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770442966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770442966", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770442966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770442966", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770442966", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770442966", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KEFFLLFTVLDENKSWYSNA", "down_seq": "QAAAMLDFRLLSEDIEGFQD", "snv": [ { "evidence": [ { "id": "rs770442966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770442966" }, { "id": "rs770442966", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770442966" }, { "id": "rs770442966", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770442966" } ], "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": "X", "chr_pos": "66198951", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N596", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.588.588", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BQS7-1.590.590", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9BQS7-1.616.616", "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": "Q9BQS7-1.598.598", "start_pos": 598, "end_pos": 598, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs17216603", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17216603", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs17216603", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs17216603", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs17216603", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17216603", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs17216603", "url": "https://www.ncbi.nlm.nih.gov/snp/rs17216603#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs17216603", "url": "http://gnomad.broadinstitute.org/awesome?query=rs17216603", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FFLLFTVLDENKSWYSNANQ", "down_seq": "AAMLDFRLLSEDIEGFQDSN", "snv": [ { "evidence": [ { "id": "rs17216603", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17216603" }, { "id": "rs17216603", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs17216603" }, { "id": "rs17216603", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17216603" }, { "id": "rs17216603", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs17216603#frequency_tab" }, { "id": "rs17216603", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs17216603" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NQA->NQT).", "chr_id": "X", "chr_pos": "66198947", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A598", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BQS7-1.588.588", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.590.590", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BQS7-1.616.616", "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": "Q9BQS7-1.632.632", "start_pos": 632, "end_pos": 632, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EGFQDSNRMHAINGFLFSNL", "down_seq": "RLDMCKGDTVAWHLLGLGTE", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "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 (NLP->NLS).", "chr_id": "23", "chr_pos": "66200569", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P632", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BQS7-1.616.616", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BQS7-1.621.621", "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": "Q9BQS7-1.722.722", "start_pos": 722, "end_pos": 722, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GSHREAGMRAIYNVSQCPGH", "down_seq": "ATPRQRYQAARIYYIMAEEV", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "23", "chr_pos": "66203450", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q722", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.714.714", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.760.760", "start_pos": 760, "end_pos": 760, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2088591658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088591658", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2088591658", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2088591658", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEVEWDYCPDRSWEREWHNQ", "down_seq": "EKDSYGYIFLSNKDGLLGSR", "snv": [ { "evidence": [ { "id": "rs2088591658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088591658" }, { "id": "rs2088591658", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2088591658" } ], "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 (NQS->NQF).", "chr_id": "X", "chr_pos": "66203565", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S760", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.758.758", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.762.762", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.762.762", "start_pos": 762, "end_pos": 762, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774270455", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774270455", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774270455", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774270455", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VEWDYCPDRSWEREWHNQSE", "down_seq": "DSYGYIFLSNKDGLLGSRYK", "snv": [ { "evidence": [ { "id": "rs774270455", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774270455" }, { "id": "rs774270455", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774270455" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KDS->NDS).", "chr_id": "X", "chr_pos": "66203572", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K762", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9BQS7-1.758.758", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.760.760", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.830.830", "start_pos": 830, "end_pos": 830, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2088898101", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088898101", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2088898101", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2088898101", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LGPLIKGEVGDILTVVFKNN", "down_seq": "SRPYSVHAHGVLESTTVWPL", "snv": [ { "evidence": [ { "id": "rs2088898101", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2088898101" }, { "id": "rs2088898101", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2088898101" } ], "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": "X", "chr_pos": "66208171", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A830", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9BQS7-1.829.829", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BQS7-1.844.844", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KSDKNRIGGTYKKTIYKEYK", "down_seq": "DSYTDEVAQPAWLGFLGPVL", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "23", "chr_pos": "66172434", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D83", "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": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.844.844", "start_pos": 844, "end_pos": 844, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752708727", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752708727", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752708727", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752708727", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752708727", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752708727#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752708727", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752708727", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VVFKNNASRPYSVHAHGVLE", "down_seq": "TTVWPLAAEPGEVVTYQWNI", "snv": [ { "evidence": [ { "id": "rs752708727", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752708727" }, { "id": "rs752708727", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752708727" }, { "id": "rs752708727", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752708727#frequency_tab" }, { "id": "rs752708727", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752708727" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (STT->NTT).", "chr_id": "X", "chr_pos": "66256178", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S844", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9BQS7-1.829.829", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BQS7-1.830.830", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.865.865", "start_pos": 865, "end_pos": 865, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2091131165", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2091131165", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2091131165", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2091131165#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TTVWPLAAEPGEVVTYQWNI", "down_seq": "ERSGPGPNDSACVSWIYYSA", "snv": [ { "evidence": [ { "id": "rs2091131165", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2091131165" }, { "id": "rs2091131165", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2091131165#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIP->NIS).", "chr_id": "X", "chr_pos": "66255064", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P865", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9BQS7-1.873.873", "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": "Q9BQS7-1.941.941", "start_pos": 941, "end_pos": 941, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1374264328", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1374264328", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1374264328", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1374264328#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1374264328", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1374264328", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FALLFLIFDENKSWYLEENV", "down_seq": "THGSQDPGSINLQDETFLES", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "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 (NVA->NVS).", "chr_id": "23", "chr_pos": "66256255", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A941", "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": "rs1374264328", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1374264328" }, { "id": "rs1374264328", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1374264328#frequency_tab" }, { "id": "rs1374264328", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1374264328" } ], "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": "X", "chr_pos": "66256255", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A941", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BQS7-1.931.931", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BQS7-1.933.933", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BQS7-1.943.943", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BQS7-1.960.960", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "Q9BQS7-1.943.943", "start_pos": 943, "end_pos": 943, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs979725612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs979725612", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs979725612", "url": "https://www.ensembl.org/id/rs979725612", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LLFLIFDENKSWYLEENVAT", "down_seq": "GSQDPGSINLQDETFLESNK", "snv": [ { "evidence": [ { "id": "rs979725612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs979725612" }, { "id": "rs979725612", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs979725612" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HGS->NGS).", "chr_id": "X", "chr_pos": "66256261", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H943", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9BQS7-1.931.931", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9BQS7-1.933.933", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BQS7-1.941.941", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BQS7-1.960.960", "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": "Q9BQS7-1.988.988", "start_pos": 988, "end_pos": 988, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "NGKLYANLRGLTMYQGERVA", "down_seq": "YMLAMGQDVDLHTIHFHAES", "snv": [ { "evidence": [ { "id": "Q9BQS7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQS7" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "W", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "66256236", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "W988", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQS7-1.1145.1145", "start_pos": 1145, "end_pos": 1145, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "iPTMnet", "id": "Q9BQS7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BQS7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQS7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALGGVVWYQHRQRKLRRNRR", "down_seq": "ILDDSFKLLSFKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BQS7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQS7" } ], "site_lbl": "Ser1145" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.1140.1140", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.1150.1150", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQS7-1.1155.1155", "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": "Q9BQS7-1.1150.1150", "start_pos": 1150, "end_pos": 1150, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "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": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "iPTMnet", "id": "Q9BQS7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQS7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BQS7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQS7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VWYQHRQRKLRRNRRSILDD", "down_seq": "FKLLSFKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BQS7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQS7" } ], "site_lbl": "Ser1150" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BQS7-1.1140.1140", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.1145.1145", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BQS7-1.1155.1155", "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": "Q9BQS7-1.1155.1155", "start_pos": 1155, "end_pos": 1155, "uniprot_canonical_ac": "Q9BQS7-1", "length": 1158, "uniprot_id": "HEPH_HUMAN", "protein_name": "Hephaestin", "refseq_ac": "NP_055614", "refseq_name": "hephaestin isoform b", "gene_name": "HEPH", "gene_names_uniprotkb": "HEPH; KIAA0698; PRO6242", "gene_names_refseq": "CPL; HEPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQRKLRRNRRSILDDSFKLL", "down_seq": "FKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BQS7", "url": "https://www.uniprot.org/uniprotkb/Q9BQS7" } ], "site_lbl": "Ser1155" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1066", "end_pos": "1077" }, { "start_pos": "1066", "end_pos": "1081" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "931", "end_pos": "931" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "965", "end_pos": "965" } ] }, { "type": "snv", "site_list": [ { "start_pos": "933", "end_pos": "933" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1098", "end_pos": "1098" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1116", "end_pos": "1116" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "760", "end_pos": "760" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "865", "end_pos": "865" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "943", "end_pos": "943" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1150", "end_pos": "1150" }, { "start_pos": "1155", "end_pos": "1155" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9BQS7-1.1140.1140", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9BQS7-1.1145.1145", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BQS7-1.1150.1150", "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": "P10072-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "P10072-1", "length": 659, "uniprot_id": "ZN875_HUMAN", "protein_name": "Zinc finger protein 875", "refseq_ac": "NP_001316692", "refseq_name": "zinc finger protein 875 isoform c", "gene_name": "ZNF875", "gene_names_uniprotkb": "ZNF875; HKR1", "gene_names_refseq": "HKR1; ZNF875", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10072", "url": "https://www.uniprot.org/uniprotkb/P10072" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P10072", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10072", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VCKECGQSFSLKSNLITHQR", "down_seq": "HTGEKPYVCRECGRGFRQHS", "snv": [ { "evidence": [ { "id": "P10072", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10072" } ], "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 (4).", "chr_id": "19", "chr_pos": "37362928", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A378", "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": "snv", "site_list": [ { "start_pos": "378", "end_pos": "378" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "642", "end_pos": "642" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P10072-1.559.559", "start_pos": 559, "end_pos": 559, "uniprot_canonical_ac": "P10072-1", "length": 659, "uniprot_id": "ZN875_HUMAN", "protein_name": "Zinc finger protein 875", "refseq_ac": "NP_001316692", "refseq_name": "zinc finger protein 875 isoform c", "gene_name": "ZNF875", "gene_names_uniprotkb": "ZNF875; HKR1", "gene_names_refseq": "HKR1; ZNF875", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10072", "url": "https://www.uniprot.org/uniprotkb/P10072" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P10072", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10072", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TLISHQRTHSGEKPFMCREC", "down_seq": "RRFRQKPNLFRHKRAHSGAF", "snv": [ { "evidence": [ { "id": "P10072", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10072" } ], "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 (3).", "chr_id": "19", "chr_pos": "37363471", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G559", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "378", "end_pos": "378" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "642", "end_pos": "642" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P10072-1.642.642", "start_pos": 642, "end_pos": 642, "uniprot_canonical_ac": "P10072-1", "length": 659, "uniprot_id": "ZN875_HUMAN", "protein_name": "Zinc finger protein 875", "refseq_ac": "NP_001316692", "refseq_name": "zinc finger protein 875 isoform c", "gene_name": "ZNF875", "gene_names_uniprotkb": "ZNF875; HKR1", "gene_names_refseq": "HKR1; ZNF875", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10072", "url": "https://www.uniprot.org/uniprotkb/P10072" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P10072", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10072", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LIRHQRTHSGEKPYICRKCG", "down_seq": "GFSRKSNLIRHQRTHSG", "snv": [ { "evidence": [ { "id": "P10072", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10072" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "37363719", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R642", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "378", "end_pos": "378" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "642", "end_pos": "642" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1582820091", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582820091", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1582820091", "url": "https://www.ensembl.org/id/rs1582820091", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KRNPEDLPVSMQQIYSNLKY", "down_seq": "VSVLNTKSNRTWSQCVTNHT", "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": "Asn182", "evidence": [ { "id": "Q9UHF4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1582820091", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582820091" }, { "id": "rs1582820091", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1582820091" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->DVS).", "chr_id": "6", "chr_pos": "137009352", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N182", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NVS->SVS).", "chr_id": "6", "chr_pos": "137009351", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N182", "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": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9UHF4-1.200.200", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9UHF4-1.202.202", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "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": "Q9UHF4-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1369985878", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369985878", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1369985878", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1369985878#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1369985878", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369985878", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SMQQIYSNLKYNVSVLNTKS", "down_seq": "RTWSQCVTNHTLVLTWLEPN", "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": "Asn191", "evidence": [ { "id": "Q9UHF4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1369985878", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369985878" }, { "id": "rs1369985878", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1369985878#frequency_tab" }, { "id": "rs1369985878", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369985878" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->KRT).", "chr_id": "6", "chr_pos": "137009323", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N191", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9UHF4-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9UHF4-1.200.200", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9UHF4-1.202.202", "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": "Q9UHF4-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1331978722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1331978722", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1331978722", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1331978722", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KYNVSVLNTKSNRTWSQCVT", "down_seq": "HTLVLTWLEPNTLYCVHVES", "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": "Asn200", "evidence": [ { "id": "Q9UHF4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1331978722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1331978722" }, { "id": "rs1331978722", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1331978722" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHT->SHT).", "chr_id": "6", "chr_pos": "137008724", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N200", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9UHF4-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.202.202", "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": "Q9UHF4-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LAAPWGRAVPCVSGGLPKPA", "down_seq": "ITFLSINMKNVLQWTPPEGL", "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": "Asn42", "evidence": [ { "id": "Q9UHF4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIT->SIT).", "chr_id": "6", "chr_pos": "137017067", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N42", "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": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.44.44", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 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": "Q9UHF4-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QGVKVTYTVQYFIYGQKKWL", "down_seq": "KSECRNINRTYCDLSAETSD", "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": "Asn83", "evidence": [ { "id": "Q9UHF4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UHF4-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9UHF4-1.91.91", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9UHF4-1.93.93", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs763356187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763356187", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763356187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763356187", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763356187", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763356187#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763356187", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763356187", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VQYFIYGQKKWLNKSECRNI", "down_seq": "RTYCDLSAETSDYEHQYYAK", "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": "Asn91", "evidence": [ { "id": "Q9UHF4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs763356187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763356187" }, { "id": "rs763356187", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763356187" }, { "id": "rs763356187", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763356187#frequency_tab" }, { "id": "rs763356187", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763356187" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->DRT).", "chr_id": "6", "chr_pos": "137011406", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N91", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763356187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763356187" }, { "id": "rs763356187", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763356187" }, { "id": "rs763356187", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763356187#frequency_tab" }, { "id": "rs763356187", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763356187" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->HRT).", "chr_id": "6", "chr_pos": "137011406", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N91", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9UHF4-1.83.83", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9UHF4-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.93.93", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs142288648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142288648", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142288648", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs142288648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142288648", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142288648#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs142288648", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142288648", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs142288648", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142288648", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs375320839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375320839", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QQIYSNLKYNVSVLNTKSNR", "down_seq": "WSQCVTNHTLVLTWLEPNTL", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" }, { "id": "rs142288648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648" }, { "id": "rs142288648", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142288648" }, { "id": "rs142288648", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648" }, { "id": "rs142288648", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142288648#frequency_tab" }, { "id": "rs142288648", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142288648" }, { "id": "rs142288648", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142288648" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-loss (NRT->NRM).", "chr_id": "6", "chr_pos": "137009318", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T193", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs375320839", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375320839" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "=", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->NR=).", "chr_id": "6", "chr_pos": "137009317", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T193", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs142288648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648" }, { "id": "rs142288648", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142288648" }, { "id": "rs142288648", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648" }, { "id": "rs142288648", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142288648#frequency_tab" }, { "id": "rs142288648", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142288648" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->NRK).", "chr_id": "6", "chr_pos": "137009318", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T193", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs142288648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648" }, { "id": "rs142288648", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142288648" }, { "id": "rs142288648", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142288648" }, { "id": "rs142288648", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142288648#frequency_tab" }, { "id": "rs142288648", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142288648" } ], "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 (NRT->NRR).", "chr_id": "6", "chr_pos": "137009318", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T193", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9UHF4-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9UHF4-1.200.200", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9UHF4-1.202.202", "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": 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": "Q9UHF4-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765880720", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765880720", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765880720", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765880720", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765880720", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765880720#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765880720", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765880720", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs765880720", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765880720", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KWKRNPEDLPVSMQQIYSNL", "down_seq": "YNVSVLNTKSNRTWSQCVTN", "snv": [ { "evidence": [ { "id": "rs765880720", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765880720" }, { "id": "rs765880720", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765880720" }, { "id": "rs765880720", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765880720#frequency_tab" }, { "id": "rs765880720", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765880720" }, { "id": "rs765880720", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765880720" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLK->NLT).", "chr_id": "6", "chr_pos": "137009357", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K180", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9UHF4-1.200.200", "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": "Q9UHF4-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RNPEDLPVSMQQIYSNLKYN", "down_seq": "SVLNTKSNRTWSQCVTNHTL", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "137009349", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V183", "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: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": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q9UHF4-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9UHF4-1.200.200", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9UHF4-1.202.202", "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": "Q9UHF4-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1249743400", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249743400", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1249743400", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1249743400#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1249743400", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249743400", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NPEDLPVSMQQIYSNLKYNV", "down_seq": "VLNTKSNRTWSQCVTNHTLV", "snv": [ { "evidence": [ { "id": "rs1249743400", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249743400" }, { "id": "rs1249743400", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1249743400#frequency_tab" }, { "id": "rs1249743400", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249743400" } ], "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 (NVS->NVP).", "chr_id": "6", "chr_pos": "137009346", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9UHF4-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9UHF4-1.200.200", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9UHF4-1.202.202", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1775389355", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1775389355", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1775389355", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1775389355", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IYSNLKYNVSVLNTKSNRTW", "down_seq": "QCVTNHTLVLTWLEPNTLYC", "snv": [ { "evidence": [ { "id": "rs1775389355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1775389355" }, { "id": "rs1775389355", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1775389355" } ], "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 (SQC->NQC).", "chr_id": "6", "chr_pos": "137009312", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S195", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9UHF4-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9UHF4-1.200.200", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9UHF4-1.202.202", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs145285325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145285325", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145285325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145285325", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145285325", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145285325#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145285325", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145285325", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs145285325", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145285325", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NVSVLNTKSNRTWSQCVTNH", "down_seq": "LVLTWLEPNTLYCVHVESFV", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" }, { "id": "rs145285325", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145285325" }, { "id": "rs145285325", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145285325" }, { "id": "rs145285325", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145285325#frequency_tab" }, { "id": "rs145285325", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145285325" }, { "id": "rs145285325", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145285325" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NHT->NHM).", "chr_id": "6", "chr_pos": "137008718", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T202", "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": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9UHF4-1.182.182", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9UHF4-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9UHF4-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9UHF4-1.191.191", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9UHF4-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9UHF4-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.200.200", "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": "Q9UHF4-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754745901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754745901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754745901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754745901", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754745901", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754745901#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754745901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754745901", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754745901", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754745901", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VPGPPRRAQPSEKQCARTLK", "down_seq": "QSSEFKAKIIFWYVLPVSIT", "snv": [ { "evidence": [ { "id": "rs754745901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754745901" }, { "id": "rs754745901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754745901" }, { "id": "rs754745901", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754745901#frequency_tab" }, { "id": "rs754745901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754745901" }, { "id": "rs754745901", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754745901" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DQS->NQS).", "chr_id": "6", "chr_pos": "137008599", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D242", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1582814690", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582814690", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1582814690", "url": "https://www.ensembl.org/id/rs1582814690", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FVPAEKIVINFITLNISDDS", "down_seq": "ISHQDMSLLGKSSDVSSLND", "snv": [ { "evidence": [ { "id": "rs1582814690", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582814690" }, { "id": "rs1582814690", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1582814690" } ], "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": "6", "chr_pos": "137002257", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K321", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9UHF4-1.326.326", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KIVINFITLNISDDSKISHQ", "down_seq": "MSLLGKSSDVSSLNDPQPSG", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DMS->NMS).", "chr_id": "6", "chr_pos": "137002244", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D326", "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": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9UHF4-1.321.321", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9UHF4-1.342.342", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ISHQDMSLLGKSSDVSSLND", "down_seq": "QPSGNLRPPQEEEEVKHLGY", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "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 (NDP->NDS).", "chr_id": "6", "chr_pos": "137002196", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P342", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9UHF4-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9UHF4-1.349.349", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.349.349", "start_pos": 349, "end_pos": 349, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1225825815", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225825815", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225825815", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225825815", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLGKSSDVSSLNDPQPSGNL", "down_seq": "PPQEEEEVKHLGYASHLMEI", "snv": [ { "evidence": [ { "id": "rs1225825815", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225825815" }, { "id": "rs1225825815", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225825815" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLR->NLS).", "chr_id": "6", "chr_pos": "137002173", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R349", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9UHF4-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9UHF4-1.369.369", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.369.369", "start_pos": 369, "end_pos": 369, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs867814689", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867814689", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs867814689", "url": "https://www.ensembl.org/id/rs867814689", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RPPQEEEEVKHLGYASHLME", "down_seq": "FCDSEENTEGTSLTQQESLS", "snv": [ { "evidence": [ { "id": "rs867814689", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867814689" }, { "id": "rs867814689", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs867814689" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IFC->NFC).", "chr_id": "6", "chr_pos": "137002114", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I369", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9UHF4-1.349.349", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.395.395", "start_pos": 395, "end_pos": 395, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ENTEGTSLTQQESLSRTIPP", "down_seq": "KTVIEYEYDVRTTDICAGPE", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "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 (DKT->NKT).", "chr_id": "6", "chr_pos": "137002037", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D395", "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": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q9UHF4-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9UHF4-1.412.412", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1420697238", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1420697238", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1420697238", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1420697238", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SRTIPPDKTVIEYEYDVRTT", "down_seq": "ICAGPEEQELSLQEEVSTQG", "snv": [ { "evidence": [ { "id": "rs1420697238", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1420697238" }, { "id": "rs1420697238", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1420697238" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DIC->NIC).", "chr_id": "6", "chr_pos": "137001995", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D409", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9UHF4-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9UHF4-1.412.412", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.412.412", "start_pos": 412, "end_pos": 412, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "IPPDKTVIEYEYDVRTTDIC", "down_seq": "GPEEQELSLQEEVSTQGTLL", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "6", "chr_pos": "137001985", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A412", "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:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UHF4-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9UHF4-1.409.409", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs764221099", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764221099", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764221099", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764221099", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764221099", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764221099#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764221099", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764221099", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "APWGRAVPCVSGGLPKPANI", "down_seq": "FLSINMKNVLQWTPPEGLQG", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "glycoeffect": [ "n-glyco-sequon-loss", "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: n-glyco-sequon-loss (NIT->NIA).", "chr_id": "6", "chr_pos": "137017062", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T44", "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": "rs764221099", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764221099" }, { "id": "rs764221099", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764221099" }, { "id": "rs764221099", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764221099#frequency_tab" }, { "id": "rs764221099", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764221099" } ], "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 (NIT->NII).", "chr_id": "6", "chr_pos": "137017061", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T44", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.42.42", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1582826062", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582826062", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1582826062", "url": "https://www.ensembl.org/id/rs1582826062", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LSINMKNVLQWTPPEGLQGV", "down_seq": "VTYTVQYFIYGQKKWLNKSE", "snv": [ { "evidence": [ { "id": "rs1582826062", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582826062" }, { "id": "rs1582826062", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1582826062" } ], "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": "6", "chr_pos": "137016994", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K66", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q9UHF4-1.83.83", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9UHF4-1.85.85", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UHF4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKVTYTVQYFIYGQKKWLNK", "down_seq": "ECRNINRTYCDLSAETSDYE", "snv": [ { "evidence": [ { "id": "Q9UHF4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UHF4" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKS->NKL).", "chr_id": "6", "chr_pos": "137011423", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S85", "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": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9UHF4-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.83.83", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9UHF4-1.91.91", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9UHF4-1.93.93", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UHF4-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "Q9UHF4-1", "length": 553, "uniprot_id": "I20RA_HUMAN", "protein_name": "Interleukin-20 receptor subunit alpha", "refseq_ac": "NP_001265651", "refseq_name": "interleukin-20 receptor subunit alpha isoform 2", "gene_name": "IL20RA", "gene_names_uniprotkb": "IL20RA; PRO1315", "gene_names_refseq": "CRF2-8; IL-20R-alpha; IL-20R1; IL-20RA; IL20RA", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UHF4", "url": "https://www.uniprot.org/uniprotkb/Q9UHF4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2548154982", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2548154982", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YFIYGQKKWLNKSECRNINR", "down_seq": "YCDLSAETSDYEHQYYAKVK", "snv": [ { "evidence": [ { "id": "rs2548154982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2548154982" } ], "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 (NRT->NRA).", "chr_id": "6", "chr_pos": "137011400", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T93", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "193", "end_pos": "193" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9UHF4-1.83.83", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9UHF4-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UHF4-1.91.91", "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": "Q3ZCQ3-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "Q3ZCQ3-1", "length": 159, "uniprot_id": "F174B_HUMAN", "protein_name": "Membrane protein FAM174B", "refseq_ac": "NP_997329", "refseq_name": "membrane protein FAM174B precursor", "gene_name": "FAM174B", "gene_names_uniprotkb": "FAM174B", "gene_names_refseq": "FAM174B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3" } ], "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" } ] }, { "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": "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": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3", "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": "rs1168215707", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1168215707", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1168215707", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1168215707#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1168215707", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1168215707", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SAPWPEPERESRPPPGPGPG", "down_seq": "TTRFGSGAAGGSGSSSSNSS", "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": "ESRPPPGPGPGNTTR", "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" } ] }, { "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": "Asn53", "evidence": [ { "id": "Q3ZCQ3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3#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": "rs1168215707", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1168215707" }, { "id": "rs1168215707", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1168215707#frequency_tab" }, { "id": "rs1168215707", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1168215707" } ], "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": "15", "chr_pos": "92655502", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N53", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "53", "end_pos": "53" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q3ZCQ3-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q3ZCQ3-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q3ZCQ3-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q3ZCQ3-1.73.73", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3ZCQ3-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "Q3ZCQ3-1", "length": 159, "uniprot_id": "F174B_HUMAN", "protein_name": "Membrane protein FAM174B", "refseq_ac": "NP_997329", "refseq_name": "membrane protein FAM174B precursor", "gene_name": "FAM174B", "gene_names_uniprotkb": "FAM174B", "gene_names_refseq": "FAM174B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "rs771719507", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771719507", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771719507", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771719507", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771719507", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771719507", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PGNTTRFGSGAAGGSGSSSS", "down_seq": "SSGDALVTRISILLRDLPTL", "glycosylation": [ { "glytoucan_ac": "G07755XJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FGSGAAGGSGSSSSnSSGDALVTR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn71", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G74381CZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FGSGAAGGSGSSSSnSSGDALVTR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn71", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "snv": [ { "evidence": [ { "id": "rs771719507", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771719507" }, { "id": "rs771719507", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771719507" }, { "id": "rs771719507", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771719507" } ], "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": "15", "chr_pos": "92655447", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N71", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "53", "end_pos": "53" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q3ZCQ3-1.53.53", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q3ZCQ3-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q3ZCQ3-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q3ZCQ3-1.73.73", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3ZCQ3-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "Q3ZCQ3-1", "length": 159, "uniprot_id": "F174B_HUMAN", "protein_name": "Membrane protein FAM174B", "refseq_ac": "NP_997329", "refseq_name": "membrane protein FAM174B precursor", "gene_name": "FAM174B", "gene_names_uniprotkb": "FAM174B", "gene_names_refseq": "FAM174B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3ZCQ3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3ZCQ3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FTTLLIACLLLRVFRSGKRL", "down_seq": "KTRKYDIITTPAERVEMAPL", "snv": [ { "evidence": [ { "id": "Q3ZCQ3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3ZCQ3" } ], "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 (KKT->NKT).", "chr_id": "15", "chr_pos": "92630327", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K121", "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": "53", "end_pos": "53" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q3ZCQ3-1.135.135", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3ZCQ3-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "Q3ZCQ3-1", "length": 159, "uniprot_id": "F174B_HUMAN", "protein_name": "Membrane protein FAM174B", "refseq_ac": "NP_997329", "refseq_name": "membrane protein FAM174B precursor", "gene_name": "FAM174B", "gene_names_uniprotkb": "FAM174B", "gene_names_refseq": "FAM174B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3ZCQ3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3ZCQ3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RSGKRLKKTRKYDIITTPAE", "down_seq": "VEMAPLNEEDDEDEDSTVFD", "snv": [ { "evidence": [ { "id": "Q3ZCQ3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3ZCQ3" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "92630287", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R135", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "53", "end_pos": "53" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q3ZCQ3-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3ZCQ3-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "Q3ZCQ3-1", "length": 159, "uniprot_id": "F174B_HUMAN", "protein_name": "Membrane protein FAM174B", "refseq_ac": "NP_997329", "refseq_name": "membrane protein FAM174B precursor", "gene_name": "FAM174B", "gene_names_uniprotkb": "FAM174B", "gene_names_refseq": "FAM174B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1318739805", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318739805", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1318739805", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1318739805", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "APWPEPERESRPPPGPGPGN", "down_seq": "TRFGSGAAGGSGSSSSNSSG", "snv": [ { "evidence": [ { "id": "rs1318739805", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318739805" }, { "id": "rs1318739805", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1318739805" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->NPT).", "chr_id": "15", "chr_pos": "92619352", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T54", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "53", "end_pos": "53" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q3ZCQ3-1.53.53", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q3ZCQ3-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q3ZCQ3-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q3ZCQ3-1.73.73", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3ZCQ3-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "Q3ZCQ3-1", "length": 159, "uniprot_id": "F174B_HUMAN", "protein_name": "Membrane protein FAM174B", "refseq_ac": "NP_997329", "refseq_name": "membrane protein FAM174B precursor", "gene_name": "FAM174B", "gene_names_uniprotkb": "FAM174B", "gene_names_refseq": "FAM174B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753312533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753312533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753312533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753312533", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753312533", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753312533#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753312533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753312533", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754447692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754447692", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754447692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754447692", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754447692", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754447692#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754447692", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754447692", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PWPEPERESRPPPGPGPGNT", "down_seq": "RFGSGAAGGSGSSSSNSSGD", "snv": [ { "evidence": [ { "id": "rs753312533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753312533" }, { "id": "rs753312533", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753312533" }, { "id": "rs753312533", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753312533#frequency_tab" }, { "id": "rs753312533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753312533" } ], "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": "15", "chr_pos": "92655496", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T55", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs754447692", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754447692" }, { "id": "rs754447692", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754447692" }, { "id": "rs754447692", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754447692#frequency_tab" }, { "id": "rs754447692", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754447692" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->NTP).", "chr_id": "15", "chr_pos": "92655497", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T55", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "53", "end_pos": "53" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q3ZCQ3-1.53.53", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q3ZCQ3-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q3ZCQ3-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q3ZCQ3-1.73.73", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "Q3ZCQ3-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "Q3ZCQ3-1", "length": 159, "uniprot_id": "F174B_HUMAN", "protein_name": "Membrane protein FAM174B", "refseq_ac": "NP_997329", "refseq_name": "membrane protein FAM174B precursor", "gene_name": "FAM174B", "gene_names_uniprotkb": "FAM174B", "gene_names_refseq": "FAM174B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3ZCQ3", "url": "https://www.uniprot.org/uniprotkb/Q3ZCQ3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1305841883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1305841883", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1305841883", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1305841883", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs501381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs501381", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs501381", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs501381", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs501381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs501381", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs501381", "url": "https://www.ncbi.nlm.nih.gov/snp/rs501381#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs501381", "url": "http://gnomad.broadinstitute.org/awesome?query=rs501381", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTTRFGSGAAGGSGSSSSNS", "down_seq": "GDALVTRISILLRDLPTLKA", "snv": [ { "evidence": [ { "id": "rs1305841883", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1305841883" }, { "id": "rs1305841883", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1305841883" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NS*).", "chr_id": "15", "chr_pos": "92619294", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S73", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs501381", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs501381" }, { "id": "rs501381", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs501381" }, { "id": "rs501381", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs501381" }, { "id": "rs501381", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs501381#frequency_tab" }, { "id": "rs501381", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs501381" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSR).", "chr_id": "15", "chr_pos": "92655441", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S73", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "53", "end_pos": "53" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q3ZCQ3-1.53.53", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q3ZCQ3-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q3ZCQ3-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q3ZCQ3-1.71.71", "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": "Q14289-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14289" } ], "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": "Q14289", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14289", "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": "Q14289", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14289" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q14289-1.9.9", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A role for Pyk2 and Src in linking G-protein-coupled receptors with MAP kinase activation.", "journal": "Nature", "date": "1996", "authors": "Dikic I, Tokiwa G, Lev S, Courtneidge SA, Schlessinger J", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "8849729", "url": "https://glygen.org/publication/PubMed/8849729" } ] }, { "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" } ] }, { "title": "Tyrosine phosphorylation of beta3 integrin provides a binding site for Pyk2.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Butler B, Blystone SD", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15695828", "url": "https://glygen.org/publication/PubMed/15695828" } ] }, { "title": "Calcineurin is essential for depolarization-induced nuclear translocation and tyrosine phosphorylation of PYK2 in neurons.", "journal": "Journal of cell science", "date": "2007", "authors": "Faure C, Corvol JC, Toutant M, Valjent E, Hvalby O, Jensen V, El Messari S, Corsi JM, Kadare G, Girault JA", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "17684059", "url": "https://glygen.org/publication/PubMed/17684059" } ] }, { "title": "Activation of protein tyrosine kinase PYK2 by the m1 muscarinic acetylcholine receptor.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "1998", "authors": "Felsch JS, Cachero TG, Peralta EG", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "9560226", "url": "https://glygen.org/publication/PubMed/9560226" } ] }, { "title": "The role of proline-rich protein tyrosine kinase 2 in differentiation-dependent signaling in human epidermal keratinocytes.", "journal": "The Journal of investigative dermatology", "date": "2007", "authors": "Schindler EM, Baumgartner M, Gribben EM, Li L, Efimova T", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "17205062", "url": "https://glygen.org/publication/PubMed/17205062" } ] }, { "title": "PYK2 autophosphorylation, but not kinase activity, is necessary for adhesion-induced association with c-Src, osteoclast spreading, and bone resorption.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Lakkakorpi PT, Bett AJ, Lipfert L, Rodan GA, Duong LT", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" } ] }, { "title": "RAFTK/Pyk2 activation is mediated by trans-acting autophosphorylation in a Src-independent manner.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Park SY, Avraham HK, Avraham S", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15166227", "url": "https://glygen.org/publication/PubMed/15166227" } ] }, { "title": "The cytoplasmic tyrosine kinase Pyk2 as a novel effector of fibroblast growth factor receptor 3 activation.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Meyer AN, Gastwirt RF, Schlaepfer DD, Donoghue DJ", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15105428", "url": "https://glygen.org/publication/PubMed/15105428" } ] }, { "title": "Nephrocystin interacts with Pyk2, p130(Cas), and tensin and triggers phosphorylation of Pyk2.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2001", "authors": "Benzing T, Gerke P, Hopker K, Hildebrandt F, Kim E, Walz G", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11493697", "url": "https://glygen.org/publication/PubMed/11493697" } ] }, { "title": "Negative regulation of PYK2/related adhesion focal tyrosine kinase signal transduction by hematopoietic tyrosine phosphatase SHPTP1.", "journal": "The Journal of biological chemistry", "date": "1999-10-22", "authors": "Kumar S, Avraham S, Bharti A, Goyal J, Pandey P, Kharbanda S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10521452", "url": "https://glygen.org/publication/PubMed/10521452" } ] }, { "title": "Protein-tyrosine kinase Pyk2 is involved in interleukin-2 production by Jurkat T cells via its tyrosine 402.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Katagiri T, Takahashi T, Sasaki T, Nakamura S, Hattori S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021" } ] }, { "title": "Cbl associates with Pyk2 and Src to regulate Src kinase activity, alpha(v)beta(3) integrin-mediated signaling, cell adhesion, and osteoclast motility.", "journal": "The Journal of cell biology", "date": "2001", "authors": "Sanjay A, Houghton A, Neff L, DiDomenico E, Bardelay C, Antoine E, Levy J, Gailit J, Bowtell D, Horne WC, Baron R", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11149930", "url": "https://glygen.org/publication/PubMed/11149930" } ] }, { "title": "Csk homologous kinase associates with RAFTK/Pyk2 in breast cancer cells and negatively regulates its activation and breast cancer cell migration.", "journal": "International journal of oncology", "date": "2002-07", "authors": "McShan Gina D, Zagozdzon Radoslaw, Park Shin-Young, Zrihan-Licht Sheila, Fu Yigong, Avraham Shalom, Avraham Hava", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12063569", "url": "https://glygen.org/publication/PubMed/12063569" } ] }, { "title": "HIV-1 gp120 and chemokine activation of Pyk2 and mitogen-activated protein kinases in primary macrophages mediated by calcium-dependent, pertussis toxin-insensitive chemokine receptor signaling.", "journal": "Blood", "date": "2001", "authors": "Del Corno M, Liu QH, Schols D, de Clercq E, Gessani S, Freedman BD, Collman RG", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" } ] }, { "title": "Glucose activates mitogen-activated protein kinase (extracellular signal-regulated kinase) through proline-rich tyrosine kinase-2 and the Glut1 glucose transporter.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Bandyopadhyay G, Sajan MP, Kanoh Y, Standaert ML, Burke TR Jr, Quon MJ, Reed BC, Dikic I, Noel LE, Newgard CB, Farese R", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11007796", "url": "https://glygen.org/publication/PubMed/11007796" } ] }, { "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924" } ] }, { "title": "Unique regulation of c-Jun N-terminal kinase by PYK2/CAK-beta in angiotensin II-stimulated vascular smooth muscle cells.", "journal": "Biochemical and biophysical research communications", "date": "2001-08-31", "authors": "Frank G D, Eguchi S, Motley E D, Sasaki T, Inagami T", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11520052", "url": "https://glygen.org/publication/PubMed/11520052" } ] }, { "title": "PYK2 as a mediator of endothelin-1/G alpha 11 signaling to GLUT4 glucose transporters.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Park JG, Bose A, Leszyk J, Czech MP", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11602570", "url": "https://glygen.org/publication/PubMed/11602570" } ] }, { "title": "Human endothelial Pyk2 is expressed in two isoforms and associates with paxillin and p130Cas.", "journal": "Biochemical and biophysical research communications", "date": "2002", "authors": "Keogh RJ, Houliston RA, Wheeler-Jones CP", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787" } ] }, { "title": "Calcitonin induces dephosphorylation of Pyk2 and phosphorylation of focal adhesion kinase in osteoclasts.", "journal": "Bone", "date": "2002", "authors": "Zhang Z, Neff L, Bothwell AL, Baron R, Horne WC", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12231407", "url": "https://glygen.org/publication/PubMed/12231407" } ] }, { "title": "Beta 3 integrin phosphorylation is essential for Arp3 organization into leukocyte alpha V beta 3-vitronectin adhesion contacts.", "journal": "Journal of cell science", "date": "2004", "authors": "Chandhoke SK, Williams M, Schaefer E, Zorn L, Blystone SD", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "14996908", "url": "https://glygen.org/publication/PubMed/14996908" } ] }, { "title": "The epidermal growth factor receptor (EGFR) and proline rich tyrosine kinase 2 (PYK2) are involved in tissue factor dependent factor VIIa signalling in HaCaT cells.", "journal": "Thrombosis and haemostasis", "date": "2004", "authors": "Wiiger MT, Prydz H", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15213840", "url": "https://glygen.org/publication/PubMed/15213840" } ] }, { "title": "Ephrin-A1 binding to CD4+ T lymphocytes stimulates migration and induces tyrosine phosphorylation of PYK2.", "journal": "Blood", "date": "2005", "authors": "Aasheim HC, Delabie J, Finne EF", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15585656", "url": "https://glygen.org/publication/PubMed/15585656" } ] }, { "title": "Focal adhesion kinase is critical for entry of Kaposi's sarcoma-associated herpesvirus into target cells.", "journal": "Journal of virology", "date": "2006", "authors": "Krishnan HH, Sharma-Walia N, Streblow DN, Naranatt PP, Chandran B", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "16414994", "url": "https://glygen.org/publication/PubMed/16414994" } ] }, { "title": "Differential regulation of Pyk2 phosphorylation at Tyr-402 and Tyr-580 in intestinal epithelial cells: roles of calcium, Src, Rho kinase, and the cytoskeleton.", "journal": "Cellular signalling", "date": "2006", "authors": "Wu SS, Jacamo RO, Vong SK, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "16574377", "url": "https://glygen.org/publication/PubMed/16574377" } ] }, { "title": "c-jun amino-terminal kinase and mitogen activated protein kinase 1/2 mediate hepatocyte growth factor-induced migration of brain endothelial cells.", "journal": "Experimental cell research", "date": "2007", "authors": "Rush S, Khan G, Bamisaiye A, Bidwell P, Leaver HA, Rizzo MT", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "17055484", "url": "https://glygen.org/publication/PubMed/17055484" } ] }, { "title": "Survival response-linked Pyk2 activation during potassium depletion-induced apoptosis of cerebellar granule neurons.", "journal": "Molecular and cellular neurosciences", "date": "2007", "authors": "Strappazzon F, Torch S, Trioulier Y, Blot B, Sadoul R, Verna JM", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "17188509", "url": "https://glygen.org/publication/PubMed/17188509" } ] }, { "title": "Calcitonin induces podosome disassembly and detachment of osteoclasts by modulating Pyk2 and Src activities.", "journal": "Bone", "date": "2007", "authors": "Shyu JF, Shih C, Tseng CY, Lin CH, Sun DT, Liu HT, Tsung HC, Chen TH, Lu RB", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "17321230", "url": "https://glygen.org/publication/PubMed/17321230" } ] }, { "title": "Glucocorticoids induce osteocyte apoptosis by blocking focal adhesion kinase-mediated survival. Evidence for inside-out signaling leading to anoikis.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Plotkin LI, Manolagas SC, Bellido T", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "17581824", "url": "https://glygen.org/publication/PubMed/17581824" } ] }, { "title": "Proline-rich tyrosine kinase 2 regulates spreading and migration of eosinophils after beta2-integrin adhesion.", "journal": "American journal of respiratory cell and molecular biology", "date": "2008", "authors": "Zhu X, Boetticher E, Wang L, Duan Y, Learoyd J, Leff AR", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "18367725", "url": "https://glygen.org/publication/PubMed/18367725" } ] }, { "title": "Endothelin (ET)-1 inhibits nicotinamide adenine dinucleotide phosphate oxidase activity in human abdominal aortic endothelial cells: a novel function of ETB1 receptors.", "journal": "Endocrinology", "date": "2008", "authors": "Dammanahalli JK, Sun Z", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "18535108", "url": "https://glygen.org/publication/PubMed/18535108" } ] }, { "title": "Dynamin reduces Pyk2 Y402 phosphorylation and SRC binding in osteoclasts.", "journal": "Molecular and cellular biology", "date": "2009", "authors": "Bruzzaniti A, Neff L, Sandoval A, Du L, Horne WC, Baron R", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19380485", "url": "https://glygen.org/publication/PubMed/19380485" } ] }, { "title": "Effects of micrometric titanium particles on osteoblast attachment and cytoskeleton architecture.", "journal": "Acta biomaterialia", "date": "2010", "authors": "Saldana L, Vilaboa N", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19861182", "url": "https://glygen.org/publication/PubMed/19861182" } ] }, { "title": "Functional activation of proline-rich tyrosine kinase2 (PYK2) in peripheral blood mononuclear cells from patients with systemic lupus erythematosus.", "journal": "BMC musculoskeletal disorders", "date": "2009", "authors": "Wang M, Sun H, Zhang W, Zhang Y", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19919693", "url": "https://glygen.org/publication/PubMed/19919693" } ] }, { "title": "The T cell receptor-mediated phosphorylation of Pyk2 tyrosines 402 and 580 occurs via a distinct mechanism than other receptor systems.", "journal": "Journal of leukocyte biology", "date": "2010", "authors": "Collins M, Tremblay M, Chapman N, Curtiss M, Rothman PB, Houtman JC", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20028775", "url": "https://glygen.org/publication/PubMed/20028775" } ] }, { "title": "TrkB is highly expressed in NSCLC and mediates BDNF-induced the activation of Pyk2 signaling and the invasion of A549 cells.", "journal": "BMC cancer", "date": "2010", "authors": "Zhang S, Guo D, Luo W, Zhang Q, Zhang Y, Li C, Lu Y, Cui Z, Qiu X", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20156366", "url": "https://glygen.org/publication/PubMed/20156366" } ] }, { "title": "Pyk2 uncouples metabotropic glutamate receptor G protein signaling but facilitates ERK1/2 activation.", "journal": "Molecular brain", "date": "2010", "authors": "Nicodemo AA, Pampillo M, Ferreira LT, Dale LB, Cregan T, Ribeiro FM, Ferguson SS", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20180987", "url": "https://glygen.org/publication/PubMed/20180987" } ] }, { "title": "The PI3K p110alpha isoform regulates endothelial adherens junctions via Pyk2 and Rac1.", "journal": "The Journal of cell biology", "date": "2010", "authors": "Cain RJ, Vanhaesebroeck B, Ridley AJ", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20308428", "url": "https://glygen.org/publication/PubMed/20308428" } ] }, { "title": "T cell receptor activation leads to two distinct phases of Pyk2 activation and actin cytoskeletal rearrangement in human T cells.", "journal": "Molecular immunology", "date": "2010", "authors": "Collins M, Bartelt RR, Houtman JC", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20381867", "url": "https://glygen.org/publication/PubMed/20381867" } ] }, { "title": "Hematopoietic Pyk2 regulates migration of differentiated HL-60 cells.", "journal": "Journal of inflammation (London, England)", "date": "2010", "authors": "Wang L, Learoyd J, Duan Y, Leff AR, Zhu X", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20507587", "url": "https://glygen.org/publication/PubMed/20507587" } ] }, { "title": "Proline-rich tyrosine kinase 2 regulates hippocampal long-term depression.", "journal": "The Journal of neuroscience : the official journal of the Society for Neuroscience", "date": "2010", "authors": "Hsin H, Kim MJ, Wang CF, Sheng M", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20826662", "url": "https://glygen.org/publication/PubMed/20826662" } ] }, { "title": "HCMV pUS28 initiates pro-migratory signaling via activation of Pyk2 kinase.", "journal": "Herpesviridae", "date": "2010", "authors": "Vomaske J, Varnum S, Melnychuk R, Smith P, Pasa-Tolic L, Shutthanandan JI, Streblow DN", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "21429240", "url": "https://glygen.org/publication/PubMed/21429240" } ] }, { "title": "Extracellular ATP acts on P2Y2 purinergic receptors to facilitate HIV-1 infection.", "journal": "The Journal of experimental medicine", "date": "2011", "authors": "Seror C, Melki MT, Subra F, Raza SQ, Bras M, Saidi H, Nardacci R, Voisin L, Paoletti A, Law F, Martins I, Amendola A, Abdul-Sater AA, Ciccosanti F, Delelis O, Niedergang F, Thierry S, Said-Sadier N, Lamaze C, Metivier D, Estaquier J, Fimia GM, Falasca L, Casetti R, Modjtahedi N, Kanellopoulos J, Mouscadet JF, Ojcius DM, Piacentini M, Gougeon ML, Kroemer G, Perfettini JL", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "21859844", "url": "https://glygen.org/publication/PubMed/21859844" } ] }, { "title": "Proline-rich tyrosine kinase 2 (Pyk2) regulates IGF-I-induced cell motility and invasion of urothelial carcinoma cells.", "journal": "PloS one", "date": "2012", "authors": "Genua M, Xu SQ, Buraschi S, Peiper SC, Gomella LG, Belfiore A, Iozzo RV, Morrione A", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "22859931", "url": "https://glygen.org/publication/PubMed/22859931" } ] }, { "title": "Non-catalytic functions of Pyk2 and Fyn regulate late stage adhesion in human T cells.", "journal": "PloS one", "date": "2012", "authors": "Chapman NM, Yoder AN, Houtman JC", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "23300847", "url": "https://glygen.org/publication/PubMed/23300847" } ] }, { "title": "HIV-1 Tat C phosphorylates VE-cadherin complex and increases human brain microvascular endothelial cell permeability.", "journal": "BMC neuroscience", "date": "2014", "authors": "Mishra R, Singh SK", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "24965120", "url": "https://glygen.org/publication/PubMed/24965120" } ] }, { "title": "PCB153-induced overexpression of ID3 contributes to the development of microvascular lesions.", "journal": "PloS one", "date": "2014", "authors": "Das JK, Felty Q", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "25090023", "url": "https://glygen.org/publication/PubMed/25090023" } ] }, { "title": "Store-operated Ca(2+) entry regulates glioma cell migration and invasion via modulation of Pyk2 phosphorylation.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2014", "authors": "Zhu M, Chen L, Zhao P, Zhou H, Zhang C, Yu S, Lin Y, Yang X", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "25433371", "url": "https://glygen.org/publication/PubMed/25433371" } ] }, { "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "25889845", "url": "https://glygen.org/publication/PubMed/25889845" } ] }, { "title": "PYK2 integrates growth factor and cytokine receptors signaling and potentiates breast cancer invasion via a positive feedback loop.", "journal": "Oncotarget", "date": "2015", "authors": "Selitrennik M, Lev S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "26084289", "url": "https://glygen.org/publication/PubMed/26084289" } ] }, { "title": "Positive and negative regulation by SLP-76/ADAP and Pyk2 of chemokine-stimulated T-lymphocyte adhesion mediated by integrin alpha4beta1.", "journal": "Molecular biology of the cell", "date": "2015", "authors": "Dios-Esponera A, Isern de Val S, Sevilla-Movilla S, Garcia-Verdugo R, Garcia-Bernal D, Arellano-Sanchez N, Cabanas C, Teixido J", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "26202465", "url": "https://glygen.org/publication/PubMed/26202465" } ] }, { "title": "The iron chelator deferasirox induces apoptosis by targeting oncogenic Pyk2/beta-catenin signaling in human multiple myeloma.", "journal": "Oncotarget", "date": "2016", "authors": "Kamihara Y, Takada K, Sato T, Kawano Y, Murase K, Arihara Y, Kikuchi S, Hayasaka N, Usami M, Iyama S, Miyanishi K, Sato Y, Kobune M, Kato J", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "27602957", "url": "https://glygen.org/publication/PubMed/27602957" } ] }, { "title": "CCL18 from ascites promotes ovarian cancer cell migration through proline-rich tyrosine kinase 2 signaling.", "journal": "Molecular cancer", "date": "2016", "authors": "Lane D, Matte I, Laplante C, Garde-Granger P, Carignan A, Bessette P, Rancourt C, Piche A", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "27613122", "url": "https://glygen.org/publication/PubMed/27613122" } ] }, { "title": "Pyk2 and FAK differentially regulate invadopodia formation and function in breast cancer cells.", "journal": "The Journal of cell biology", "date": "2018", "authors": "Genna A, Lapetina S, Lukic N, Twafra S, Meirson T, Sharma VP, Condeelis JS, Gil-Henn H", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29133485", "url": "https://glygen.org/publication/PubMed/29133485" } ] }, { "title": "Global Identification of Small Ubiquitin-related Modifier (SUMO) Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration.", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Uzoma I, Hu J, Cox E, Xia S, Zhou J, Rho HS, Guzzo C, Paul C, Ajala O, Goodwin CR, Jeong J, Moore C, Zhang H, Meluh P, Blackshaw S, Matunis M, Qian J, Zhu H", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" } ] }, { "title": "Curcumin modulation of the activation of PYK2 in peripheral blood mononuclear cells from patients with lupus nephritis.", "journal": "Reumatologia", "date": "2017", "authors": "Wang M, Zhou G, Lv J, Zeng P, Guo C, Wang Q", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29491534", "url": "https://glygen.org/publication/PubMed/29491534" } ] }, { "title": "Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer.", "journal": "PLoS computational biology", "date": "2018", "authors": "Shin SY, Muller AK, Verma N, Lev S, Nguyen LK", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29920512", "url": "https://glygen.org/publication/PubMed/29920512" } ] }, { "title": "The human ion channel TRPM2 modulates neuroblastoma cell survival and mitochondrial function through Pyk2, CREB, and MCU activation.", "journal": "American journal of physiology. Cell physiology", "date": "2018", "authors": "Hirschler-Laszkiewicz I, Chen SJ, Bao L, Wang J, Zhang XQ, Shanmughapriya S, Keefer K, Madesh M, Cheung JY, Miller BA", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "30020827", "url": "https://glygen.org/publication/PubMed/30020827" } ] }, { "title": "PYK2 negatively regulates the Hippo pathway in TNBC by stabilizing TAZ protein.", "journal": "Cell death & disease", "date": "2018", "authors": "Kedan A, Verma N, Saroha A, Shreberk-Shaked M, Muller AK, Nair NU, Lev S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "30250159", "url": "https://glygen.org/publication/PubMed/30250159" } ] }, { "title": "Tyrosine kinase Pyk2 is involved in colonic smooth muscle contraction via the RhoA/ROCK pathway.", "journal": "Physiological research", "date": "2019", "authors": "Tong L, Ao JP, Lu HL, Huang X, Zang JY, Liu SH, Song NN, Huang SQ, Lu C, Chen J, Xu WX", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "30433799", "url": "https://glygen.org/publication/PubMed/30433799" } ] }, { "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "30571746", "url": "https://glygen.org/publication/PubMed/30571746" } ] }, { "title": "Membranous NOX5-derived ROS oxidizes and activates local Src to promote malignancy of tumor cells.", "journal": "Signal transduction and targeted therapy", "date": "2020-08-14", "authors": "Chen Jie, Wang Yan, Zhang Weimin, Zhao Di, Zhang Lingyuan, Fan Jiawen, Li Jinting, Zhan Qimin", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "32792487", "url": "https://glygen.org/publication/PubMed/32792487" } ] }, { "title": "Proline-rich tyrosine kinase 2 mediates transforming growth factor-beta-induced hepatic stellate cell activation and liver fibrosis.", "journal": "Scientific reports", "date": "2020-12-03", "authors": "Kim Jonghwa, Kang Wonseok, Kang So Hee, Park Su Hyun, Kim Ji Young, Yang Sera, Ha Sang Yun, Paik Yong-Han", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" } ] }, { "title": "A PKC\u03b2-LYN-PYK2 Signaling Axis Is Critical for MCP-1-Dependent Migration and Adhesion of Monocytes.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2021-01-01", "authors": "Das Pradip, Pal Srabani, Oldfield Claudine M, Thillai Kowsalya, Bala Sinjini, Carnevale Kevin A, Cathcart Martha K, Bhattacharjee Ashish", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "33277387", "url": "https://glygen.org/publication/PubMed/33277387" } ] }, { "title": "The AXL-PYK2-PKCalpha axis as a nexus of stemness circuits in TNBC.", "journal": "Life science alliance", "date": "2021", "authors": "Khera L, Vinik Y, Maina F, Lev S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "33785524", "url": "https://glygen.org/publication/PubMed/33785524" } ] }, { "title": "The related adhesion focal tyrosine kinase differentially phosphorylates p130Cas and the Cas-like protein, p105HEF1.", "journal": "The Journal of biological chemistry", "date": "1997", "authors": "Astier A, Manie SN, Avraham H, Hirai H, Law SF, Zhang Y, Golemis EA, Fu Y, Druker BJ, Haghayeghi N, Freedman AS, Avraham S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "9242628", "url": "https://glygen.org/publication/PubMed/9242628" } ] }, { "title": "Interaction of Pyk2 and PTP-PEST with leupaxin in prostate cancer cells.", "journal": "American journal of physiology. Cell physiology", "date": "2007", "authors": "Sahu SN, Nunez S, Bai G, Gupta A", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "17329398", "url": "https://glygen.org/publication/PubMed/17329398" } ] }, { "title": "A Pyk2-Vav1 complex is recruited to beta3-adhesion sites to initiate Rho activation.", "journal": "The Biochemical journal", "date": "2009", "authors": "Gao C, Blystone SD", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19207108", "url": "https://glygen.org/publication/PubMed/19207108" } ] }, { "title": "Recruitment of Pyk2 to SHPS-1 signaling complex is required for IGF-I-dependent mitogenic signaling in vascular smooth muscle cells.", "journal": "Cellular and molecular life sciences : CMLS", "date": "2010", "authors": "Shen X, Xi G, Radhakrishnan Y, Clemmons DR", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8849729", "url": "https://glygen.org/publication/PubMed/8849729", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15695828", "url": "https://glygen.org/publication/PubMed/15695828", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17684059", "url": "https://glygen.org/publication/PubMed/17684059", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9560226", "url": "https://glygen.org/publication/PubMed/9560226", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17205062", "url": "https://glygen.org/publication/PubMed/17205062", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15166227", "url": "https://glygen.org/publication/PubMed/15166227", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15105428", "url": "https://glygen.org/publication/PubMed/15105428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11493697", "url": "https://glygen.org/publication/PubMed/11493697", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q14289*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "10521452", "url": "https://glygen.org/publication/PubMed/10521452", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11149930", "url": "https://glygen.org/publication/PubMed/11149930", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12063569", "url": "https://glygen.org/publication/PubMed/12063569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289", "database": "PRO", "categories": [ "Other" ] }, { "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11007796", "url": "https://glygen.org/publication/PubMed/11007796", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11520052", "url": "https://glygen.org/publication/PubMed/11520052", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11602570", "url": "https://glygen.org/publication/PubMed/11602570", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12231407", "url": "https://glygen.org/publication/PubMed/12231407", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14996908", "url": "https://glygen.org/publication/PubMed/14996908", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15213840", "url": "https://glygen.org/publication/PubMed/15213840", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15585656", "url": "https://glygen.org/publication/PubMed/15585656", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16414994", "url": "https://glygen.org/publication/PubMed/16414994", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16574377", "url": "https://glygen.org/publication/PubMed/16574377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17055484", "url": "https://glygen.org/publication/PubMed/17055484", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17188509", "url": "https://glygen.org/publication/PubMed/17188509", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17321230", "url": "https://glygen.org/publication/PubMed/17321230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17581824", "url": "https://glygen.org/publication/PubMed/17581824", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18367725", "url": "https://glygen.org/publication/PubMed/18367725", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18535108", "url": "https://glygen.org/publication/PubMed/18535108", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19380485", "url": "https://glygen.org/publication/PubMed/19380485", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19861182", "url": "https://glygen.org/publication/PubMed/19861182", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19919693", "url": "https://glygen.org/publication/PubMed/19919693", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20028775", "url": "https://glygen.org/publication/PubMed/20028775", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20156366", "url": "https://glygen.org/publication/PubMed/20156366", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20180987", "url": "https://glygen.org/publication/PubMed/20180987", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20308428", "url": "https://glygen.org/publication/PubMed/20308428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20381867", "url": "https://glygen.org/publication/PubMed/20381867", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20507587", "url": "https://glygen.org/publication/PubMed/20507587", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20826662", "url": "https://glygen.org/publication/PubMed/20826662", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21429240", "url": "https://glygen.org/publication/PubMed/21429240", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21859844", "url": "https://glygen.org/publication/PubMed/21859844", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22859931", "url": "https://glygen.org/publication/PubMed/22859931", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23300847", "url": "https://glygen.org/publication/PubMed/23300847", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24965120", "url": "https://glygen.org/publication/PubMed/24965120", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25090023", "url": "https://glygen.org/publication/PubMed/25090023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25433371", "url": "https://glygen.org/publication/PubMed/25433371", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25889845", "url": "https://glygen.org/publication/PubMed/25889845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26084289", "url": "https://glygen.org/publication/PubMed/26084289", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26202465", "url": "https://glygen.org/publication/PubMed/26202465", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27602957", "url": "https://glygen.org/publication/PubMed/27602957", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27613122", "url": "https://glygen.org/publication/PubMed/27613122", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29133485", "url": "https://glygen.org/publication/PubMed/29133485", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29491534", "url": "https://glygen.org/publication/PubMed/29491534", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29920512", "url": "https://glygen.org/publication/PubMed/29920512", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30020827", "url": "https://glygen.org/publication/PubMed/30020827", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30250159", "url": "https://glygen.org/publication/PubMed/30250159", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30433799", "url": "https://glygen.org/publication/PubMed/30433799", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30571746", "url": "https://glygen.org/publication/PubMed/30571746", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32792487", "url": "https://glygen.org/publication/PubMed/32792487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33277387", "url": "https://glygen.org/publication/PubMed/33277387", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33785524", "url": "https://glygen.org/publication/PubMed/33785524", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9242628", "url": "https://glygen.org/publication/PubMed/9242628", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17329398", "url": "https://glygen.org/publication/PubMed/17329398", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19207108", "url": "https://glygen.org/publication/PubMed/19207108", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LNLEARRSHLSESCSIESDI", "down_seq": "AEIPDETLRRPGGPQYGIAR", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Abolishes autophosphorylation. Abolishes interaction with SRC.", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "8849729", "url": "https://glygen.org/publication/PubMed/8849729" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" }, { "database": "PubMed", "id": "15695828", "url": "https://glygen.org/publication/PubMed/15695828" } ], "site_lbl": "Tyr402" }, { "kinase_uniprot_canonical_ac": "Q14289-1", "kinase_gene_name": "PTK2B", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "17684059", "url": "https://glygen.org/publication/PubMed/17684059" }, { "database": "PubMed", "id": "9560226", "url": "https://glygen.org/publication/PubMed/9560226" }, { "database": "PubMed", "id": "17205062", "url": "https://glygen.org/publication/PubMed/17205062" }, { "database": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" }, { "database": "PubMed", "id": "15166227", "url": "https://glygen.org/publication/PubMed/15166227" }, { "database": "PubMed", "id": "15105428", "url": "https://glygen.org/publication/PubMed/15105428" }, { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "11493697", "url": "https://glygen.org/publication/PubMed/11493697" } ], "site_lbl": "Tyr402" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by autocatalysis", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "IntAct", "id": "Q14289", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q14289*" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "10521452", "url": "https://glygen.org/publication/PubMed/10521452" }, { "database": "PubMed", "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021" }, { "database": "PubMed", "id": "11149930", "url": "https://glygen.org/publication/PubMed/11149930" }, { "database": "PubMed", "id": "12063569", "url": "https://glygen.org/publication/PubMed/12063569" }, { "database": "PubMed", "id": "8849729", "url": "https://glygen.org/publication/PubMed/8849729" }, { "database": "PRO", "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289" }, { "database": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" }, { "database": "PubMed", "id": "11007796", "url": "https://glygen.org/publication/PubMed/11007796" }, { "database": "PubMed", "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924" }, { "database": "PubMed", "id": "11493697", "url": "https://glygen.org/publication/PubMed/11493697" }, { "database": "PubMed", "id": "11520052", "url": "https://glygen.org/publication/PubMed/11520052" }, { "database": "PubMed", "id": "11602570", "url": "https://glygen.org/publication/PubMed/11602570" }, { "database": "PubMed", "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787" }, { "database": "PubMed", "id": "12231407", "url": "https://glygen.org/publication/PubMed/12231407" }, { "database": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" }, { "database": "PubMed", "id": "14996908", "url": "https://glygen.org/publication/PubMed/14996908" }, { "database": "PubMed", "id": "15105428", "url": "https://glygen.org/publication/PubMed/15105428" }, { "database": "PubMed", "id": "15213840", "url": "https://glygen.org/publication/PubMed/15213840" }, { "database": "PubMed", "id": "15585656", "url": "https://glygen.org/publication/PubMed/15585656" }, { "database": "PubMed", "id": "15695828", "url": "https://glygen.org/publication/PubMed/15695828" }, { "database": "PubMed", "id": "16414994", "url": "https://glygen.org/publication/PubMed/16414994" }, { "database": "PubMed", "id": "16574377", "url": "https://glygen.org/publication/PubMed/16574377" }, { "database": "PubMed", "id": "17055484", "url": "https://glygen.org/publication/PubMed/17055484" }, { "database": "PubMed", "id": "17188509", "url": "https://glygen.org/publication/PubMed/17188509" }, { "database": "PubMed", "id": "17321230", "url": "https://glygen.org/publication/PubMed/17321230" }, { "database": "PubMed", "id": "17581824", "url": "https://glygen.org/publication/PubMed/17581824" }, { "database": "PubMed", "id": "18367725", "url": "https://glygen.org/publication/PubMed/18367725" }, { "database": "PubMed", "id": "18535108", "url": "https://glygen.org/publication/PubMed/18535108" }, { "database": "PubMed", "id": "19380485", "url": "https://glygen.org/publication/PubMed/19380485" }, { "database": "PubMed", "id": "19861182", "url": "https://glygen.org/publication/PubMed/19861182" }, { "database": "PubMed", "id": "19919693", "url": "https://glygen.org/publication/PubMed/19919693" }, { "database": "PubMed", "id": "20028775", "url": "https://glygen.org/publication/PubMed/20028775" }, { "database": "PubMed", "id": "20156366", "url": "https://glygen.org/publication/PubMed/20156366" }, { "database": "PubMed", "id": "20180987", "url": "https://glygen.org/publication/PubMed/20180987" }, { "database": "PubMed", "id": "20308428", "url": "https://glygen.org/publication/PubMed/20308428" }, { "database": "PubMed", "id": "20381867", "url": "https://glygen.org/publication/PubMed/20381867" }, { "database": "PubMed", "id": "20507587", "url": "https://glygen.org/publication/PubMed/20507587" }, { "database": "PubMed", "id": "20826662", "url": "https://glygen.org/publication/PubMed/20826662" }, { "database": "PubMed", "id": "21429240", "url": "https://glygen.org/publication/PubMed/21429240" }, { "database": "PubMed", "id": "21859844", "url": "https://glygen.org/publication/PubMed/21859844" }, { "database": "PubMed", "id": "22859931", "url": "https://glygen.org/publication/PubMed/22859931" }, { "database": "PubMed", "id": "23300847", "url": "https://glygen.org/publication/PubMed/23300847" }, { "database": "PubMed", "id": "24965120", "url": "https://glygen.org/publication/PubMed/24965120" }, { "database": "PubMed", "id": "25090023", "url": "https://glygen.org/publication/PubMed/25090023" }, { "database": "PubMed", "id": "25433371", "url": "https://glygen.org/publication/PubMed/25433371" }, { "database": "PubMed", "id": "25889845", "url": "https://glygen.org/publication/PubMed/25889845" }, { "database": "PubMed", "id": "26084289", "url": "https://glygen.org/publication/PubMed/26084289" }, { "database": "PubMed", "id": "26202465", "url": "https://glygen.org/publication/PubMed/26202465" }, { "database": "PubMed", "id": "27602957", "url": "https://glygen.org/publication/PubMed/27602957" }, { "database": "PubMed", "id": "27613122", "url": "https://glygen.org/publication/PubMed/27613122" }, { "database": "PubMed", "id": "29133485", "url": "https://glygen.org/publication/PubMed/29133485" }, { "database": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" }, { "database": "PubMed", "id": "29491534", "url": "https://glygen.org/publication/PubMed/29491534" }, { "database": "PubMed", "id": "29920512", "url": "https://glygen.org/publication/PubMed/29920512" }, { "database": "PubMed", "id": "30020827", "url": "https://glygen.org/publication/PubMed/30020827" }, { "database": "PubMed", "id": "30250159", "url": "https://glygen.org/publication/PubMed/30250159" }, { "database": "PubMed", "id": "30433799", "url": "https://glygen.org/publication/PubMed/30433799" }, { "database": "PubMed", "id": "30571746", "url": "https://glygen.org/publication/PubMed/30571746" }, { "database": "PubMed", "id": "32792487", "url": "https://glygen.org/publication/PubMed/32792487" }, { "database": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" }, { "database": "PubMed", "id": "33277387", "url": "https://glygen.org/publication/PubMed/33277387" }, { "database": "PubMed", "id": "33785524", "url": "https://glygen.org/publication/PubMed/33785524" }, { "database": "PubMed", "id": "9242628", "url": "https://glygen.org/publication/PubMed/9242628" }, { "database": "PubMed", "id": "15166227", "url": "https://glygen.org/publication/PubMed/15166227" }, { "database": "PubMed", "id": "17329398", "url": "https://glygen.org/publication/PubMed/17329398" }, { "database": "PubMed", "id": "19207108", "url": "https://glygen.org/publication/PubMed/19207108" }, { "database": "PubMed", "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079" } ], "site_lbl": "Tyr402" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14289-1.389.389", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14289-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14289-1.396.396", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14289-1.399.399", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 70 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "RAFTK/Pyk2 activation is mediated by trans-acting autophosphorylation in a Src-independent manner.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Park SY, Avraham HK, Avraham S", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15166227", "url": "https://glygen.org/publication/PubMed/15166227" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15166227", "url": "https://glygen.org/publication/PubMed/15166227", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GEVYEGVYTNHKGEKINVAV", "down_seq": "TCKKDCTLDNKEKFMSEAVI", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Abolishes kinase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "15166227", "url": "https://glygen.org/publication/PubMed/15166227" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q14289-1.473.473", "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": "Q14289-1.859.859", "start_pos": 859, "end_pos": 859, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Nephrocystin interacts with Pyk2, p130(Cas), and tensin and triggers phosphorylation of Pyk2.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2001", "authors": "Benzing T, Gerke P, Hopker K, Hildebrandt F, Kim E, Walz G", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11493697", "url": "https://glygen.org/publication/PubMed/11493697" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11493697", "url": "https://glygen.org/publication/PubMed/11493697", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SPLTPEKEVGYLEFTGPPQK", "down_seq": "PRLGAQSIQPTANLDRTDDL", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "Loss of interaction with NPHP1.", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "11493697", "url": "https://glygen.org/publication/PubMed/11493697" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14289-1.839.839", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14289-1.842.842", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14289-1.849.849", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14289-1.864.864", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14289-1.866.866", "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": "Q14289-1.881.881", "start_pos": 881, "end_pos": 881, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Recruitment of Pyk2 to SHPS-1 signaling complex is required for IGF-I-dependent mitogenic signaling in vascular smooth muscle cells.", "journal": "Cellular and molecular life sciences : CMLS", "date": "2010", "authors": "Shen X, Xi G, Radhakrishnan Y, Clemmons DR", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079" } ] }, { "title": "Activation of protein tyrosine kinase PYK2 by the m1 muscarinic acetylcholine receptor.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "1998", "authors": "Felsch JS, Cachero TG, Peralta EG", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "9560226", "url": "https://glygen.org/publication/PubMed/9560226" } ] }, { "title": "Characterization of RAFTK, a novel focal adhesion kinase, and its integrin-dependent phosphorylation and activation in megakaryocytes.", "journal": "Blood", "date": "1996-07-15", "authors": "Li J, Avraham H, Rogers R A, Raja S, Avraham S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "8695788", "url": "https://glygen.org/publication/PubMed/8695788" } ] }, { "title": "HIV-1 gp120 and chemokine activation of Pyk2 and mitogen-activated protein kinases in primary macrophages mediated by calcium-dependent, pertussis toxin-insensitive chemokine receptor signaling.", "journal": "Blood", "date": "2001", "authors": "Del Corno M, Liu QH, Schols D, de Clercq E, Gessani S, Freedman BD, Collman RG", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" } ] }, { "title": "Protein-tyrosine kinase Pyk2 is involved in interleukin-2 production by Jurkat T cells via its tyrosine 402.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Katagiri T, Takahashi T, Sasaki T, Nakamura S, Hattori S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021" } ] }, { "title": "Glucose activates mitogen-activated protein kinase (extracellular signal-regulated kinase) through proline-rich tyrosine kinase-2 and the Glut1 glucose transporter.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Bandyopadhyay G, Sajan MP, Kanoh Y, Standaert ML, Burke TR Jr, Quon MJ, Reed BC, Dikic I, Noel LE, Newgard CB, Farese R", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11007796", "url": "https://glygen.org/publication/PubMed/11007796" } ] }, { "title": "Human endothelial Pyk2 is expressed in two isoforms and associates with paxillin and p130Cas.", "journal": "Biochemical and biophysical research communications", "date": "2002", "authors": "Keogh RJ, Houliston RA, Wheeler-Jones CP", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787" } ] }, { "title": "PYK2 autophosphorylation, but not kinase activity, is necessary for adhesion-induced association with c-Src, osteoclast spreading, and bone resorption.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Lakkakorpi PT, Bett AJ, Lipfert L, Rodan GA, Duong LT", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" } ] }, { "title": "Differential regulation of cell migration and proliferation through proline-rich tyrosine kinase 2 in endothelial cells.", "journal": "Endocrinology", "date": "2004-07", "authors": "Kuwabara Koichiro, Nakaoka Takashi, Sato Kaori, Nishishita Toshihide, Sasaki Terukatsu, Yamashita Naohide", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15070849", "url": "https://glygen.org/publication/PubMed/15070849" } ] }, { "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15126359", "url": "https://glygen.org/publication/PubMed/15126359" } ] }, { "title": "PYK2 mediates anti-apoptotic AKT signaling in response to benzo[a]pyrene diol epoxide in mammary epithelial cells.", "journal": "Carcinogenesis", "date": "2006", "authors": "Burdick AD, Ivnitski-Steele ID, Lauer FT, Burchiel SW", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "16774943", "url": "https://glygen.org/publication/PubMed/16774943" } ] }, { "title": "Proline-rich tyrosine kinase 2 and its phosphorylated form pY881 are novel prognostic markers for non-small-cell lung cancer progression and patients' overall survival.", "journal": "British journal of cancer", "date": "2013", "authors": "Kuang BH, Zhang MQ, Xu LH, Hu LJ, Wang HB, Zhao WF, Du Y, Zhang X", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "23922106", "url": "https://glygen.org/publication/PubMed/23922106" } ] }, { "title": "Global Identification of Small Ubiquitin-related Modifier (SUMO) Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration.", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Uzoma I, Hu J, Cox E, Xia S, Zhou J, Rho HS, Guzzo C, Paul C, Ajala O, Goodwin CR, Jeong J, Moore C, Zhang H, Meluh P, Blackshaw S, Matunis M, Qian J, Zhu H", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" } ] }, { "title": "Proline-rich tyrosine kinase 2 mediates transforming growth factor-beta-induced hepatic stellate cell activation and liver fibrosis.", "journal": "Scientific reports", "date": "2020-12-03", "authors": "Kim Jonghwa, Kang Wonseok, Kang So Hee, Park Su Hyun, Kim Ji Young, Yang Sera, Ha Sang Yun, Paik Yong-Han", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "9560226", "url": "https://glygen.org/publication/PubMed/9560226", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q14289*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "8695788", "url": "https://glygen.org/publication/PubMed/8695788", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289", "database": "PRO", "categories": [ "Other" ] }, { "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11007796", "url": "https://glygen.org/publication/PubMed/11007796", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15070849", "url": "https://glygen.org/publication/PubMed/15070849", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15126359", "url": "https://glygen.org/publication/PubMed/15126359", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16774943", "url": "https://glygen.org/publication/PubMed/16774943", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23922106", "url": "https://glygen.org/publication/PubMed/23922106", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RLGAQSIQPTANLDRTDDLV", "down_seq": "LNVMELVRAVLELKNELCQL", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Loss of phosphorylation site. Strongly reduced interaction with GRB2.", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079" } ], "site_lbl": "Tyr881" }, { "kinase_uniprot_canonical_ac": "Q14289-1", "kinase_gene_name": "PTK2B", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "9560226", "url": "https://glygen.org/publication/PubMed/9560226" } ], "site_lbl": "Tyr881" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by SRC", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "IntAct", "id": "Q14289", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q14289*" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "8695788", "url": "https://glygen.org/publication/PubMed/8695788" }, { "database": "PRO", "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289" }, { "database": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" }, { "database": "PubMed", "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021" }, { "database": "PubMed", "id": "11007796", "url": "https://glygen.org/publication/PubMed/11007796" }, { "database": "PubMed", "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787" }, { "database": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" }, { "database": "PubMed", "id": "15070849", "url": "https://glygen.org/publication/PubMed/15070849" }, { "database": "PubMed", "id": "15126359", "url": "https://glygen.org/publication/PubMed/15126359" }, { "database": "PubMed", "id": "16774943", "url": "https://glygen.org/publication/PubMed/16774943" }, { "database": "PubMed", "id": "20521079", "url": "https://glygen.org/publication/PubMed/20521079" }, { "database": "PubMed", "id": "23922106", "url": "https://glygen.org/publication/PubMed/23922106" }, { "database": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" }, { "database": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" } ], "site_lbl": "Tyr881" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14289-1.864.864", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q14289-1.866.866", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14289-1.889.889", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14289-1.893.893", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VQDKYECLHVEAEWRYDLQI", "down_seq": "YLPEDFMESLKEDRTTLLYF", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "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 (4).", "chr_id": "8", "chr_pos": "27420673", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R134", "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": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KEDRTTLLYFYQQLRNDYMQ", "down_seq": "YASKVSEGMALQLGCLELRR", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "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 (4).", "chr_id": "8", "chr_pos": "27422325", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R165", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.247.247", "start_pos": 247, "end_pos": 247, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "FRKMIQQTFQQYASLREEEC", "down_seq": "MKFFNTLAGFANIDQETYRC", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "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": "8", "chr_pos": "27430945", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V247", "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: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": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q14289-1.266.266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CVMKFFNTLAGFANIDQETY", "down_seq": "CELIQGWNITVDLVIGPKGI", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "27431003", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R266", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14289-1.247.247", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.612.612", "start_pos": 612, "end_pos": 612, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MSPESINFRRFTTASDVWMF", "down_seq": "VCMWEILSFGKQPFFWLENK", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "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": "8", "chr_pos": "27439398", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A612", "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: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": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.660.660", "start_pos": 660, "end_pos": 660, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KGDRLPKPDLCPPVLYTLMT", "down_seq": "CWDYDPSDRPRFTELVCSLS", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "27440381", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R660", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q14289-1.664.664", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14289-1.671.671", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.664.664", "start_pos": 664, "end_pos": 664, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LPKPDLCPPVLYTLMTRCWD", "down_seq": "DPSDRPRFTELVCSLSDVYQ", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "8", "chr_pos": "27440393", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y664", "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" } ] }, { "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": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q14289-1.660.660", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14289-1.671.671", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.671.671", "start_pos": 671, "end_pos": 671, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PPVLYTLMTRCWDYDPSDRP", "down_seq": "FTELVCSLSDVYQMEKDIAM", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "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 (4).", "chr_id": "8", "chr_pos": "27440413", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R671", "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:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q14289-1.660.660", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14289-1.664.664", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14289-1.805.805", "start_pos": 805, "end_pos": 805, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IQPSSREEAQQLWEAEKVKM", "down_seq": "QILDKQQKQMVEDYQWLRQE", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "8", "chr_pos": "27450821", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R805", "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": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q14289-1.819.819", "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": "Q14289-1.864.864", "start_pos": 864, "end_pos": 864, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EKEVGYLEFTGPPQKPPRLG", "down_seq": "QSIQPTANLDRTDDLVYLNV", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "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": "8", "chr_pos": "27453155", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A864", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14289-1.849.849", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14289-1.859.859", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14289-1.866.866", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14289-1.881.881", "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": "Q14289-1.889.889", "start_pos": 889, "end_pos": 889, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PTANLDRTDDLVYLNVMELV", "down_seq": "AVLELKNELCQLPPEGYVVV", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "8", "chr_pos": "27454223", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R889", "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: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" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14289-1.881.881", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14289-1.893.893", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14289-1.906.906", "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": "Q14289-1.893.893", "start_pos": 893, "end_pos": 893, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14289", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LDRTDDLVYLNVMELVRAVL", "down_seq": "LKNELCQLPPEGYVVVVKNV", "snv": [ { "evidence": [ { "id": "Q14289", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14289" } ], "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": "8", "chr_pos": "27454235", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E893", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14289-1.881.881", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14289-1.889.889", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14289-1.906.906", "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": "Q14289-1.361.361", "start_pos": 361, "end_pos": 361, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AENMADLIDGYCRLQGEHQG", "down_seq": "LIIHPRKDGEKRNSLPQIPM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Ser361" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q14289-1.375.375", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" } ] }, { "title": "Phosphoproteome of resting human platelets.", "journal": "Journal of proteome research", "date": "2008", "authors": "Zahedi RP, Lewandrowski U, Wiesner J, Wortelkamp S, Moebius J, Schutz C, Walter U, Gambaryan S, Sickmann A", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" } ] }, { "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "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": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "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": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] }, { "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087", "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": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGEHQGSLIIHPRKDGEKRN", "down_seq": "LPQIPMLNLEARRSHLSESC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q14289-1", "kinase_gene_name": "PTK2B", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" }, { "database": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" }, { "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": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Ser375" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" }, { "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Ser375" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14289-1.361.361", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14289-1.389.389", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14289-1.394.394", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "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": "DGEKRNSLPQIPMLNLEARR", "down_seq": "HLSESCSIESDIYAEIPDET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser389" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14289-1.375.375", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14289-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14289-1.396.396", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14289-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14289-1.402.402", "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": "Q14289-1.394.394", "start_pos": 394, "end_pos": 394, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "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": "NSLPQIPMLNLEARRSHLSE", "down_seq": "CSIESDIYAEIPDETLRRPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser394" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14289-1.375.375", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14289-1.389.389", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14289-1.396.396", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14289-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14289-1.402.402", "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": "Q14289-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Serine 396 of PDK1 is required for maximal PKB activation.", "journal": "Cellular signalling", "date": "2008", "authors": "Moon Z, Wang Y, Aryan N, Mousseau DD, Scheid MP", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "18718528", "url": "https://glygen.org/publication/PubMed/18718528" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18718528", "url": "https://glygen.org/publication/PubMed/18718528", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPQIPMLNLEARRSHLSESC", "down_seq": "IESDIYAEIPDETLRRPGGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18718528", "url": "https://glygen.org/publication/PubMed/18718528" } ], "site_lbl": "Ser396" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q14289-1.389.389", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14289-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14289-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14289-1.402.402", "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": "Q14289-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "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": "IPMLNLEARRSHLSESCSIE", "down_seq": "DIYAEIPDETLRRPGGPQYG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser399" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14289-1.389.389", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14289-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14289-1.396.396", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14289-1.402.402", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.473.473", "start_pos": 473, "end_pos": 473, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Oxidative stress disrupts insulin-induced cellular redistribution of insulin receptor substrate-1 and phosphatidylinositol 3-kinase in 3T3-L1 adipocytes. A putative cellular mechanism for impaired protein kinase B activation and GLUT4 translocation.", "journal": "The Journal of biological chemistry", "date": "1999-04-09", "authors": "Tirosh A, Potashnik R, Bashan N, Rudich A", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10187855", "url": "https://glygen.org/publication/PubMed/10187855" } ] }, { "title": "Mechanism of protein kinase B activation by cyclic AMP-dependent protein kinase.", "journal": "Molecular and cellular biology", "date": "1999", "authors": "Filippa N, Sable CL, Filloux C, Hemmings B, Van Obberghen E", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10373549", "url": "https://glygen.org/publication/PubMed/10373549" } ] }, { "title": "The dynamics of protein kinase B regulation during B cell antigen receptor engagement.", "journal": "The Journal of cell biology", "date": "1999", "authors": "Astoul E, Watton S, Cantrell D", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10385529", "url": "https://glygen.org/publication/PubMed/10385529" } ] }, { "title": "Integrin-linked kinase regulates phosphorylation of serine 473 of protein kinase B by an indirect mechanism.", "journal": "Oncogene", "date": "1999", "authors": "Lynch DK, Ellis CA, Edwards PA, Hiles ID", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10637513", "url": "https://glygen.org/publication/PubMed/10637513" } ] }, { "title": "Ceramide inhibits protein kinase B/Akt by promoting dephosphorylation of serine 473.", "journal": "The Journal of biological chemistry", "date": "2000-05-05", "authors": "Schubert K M, Scheid M P, Duronio V", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10788440", "url": "https://glygen.org/publication/PubMed/10788440" } ] }, { "title": "Insulin-stimulated protein kinase B phosphorylation on Ser-473 is independent of its activity and occurs through a staurosporine-insensitive kinase.", "journal": "The Journal of biological chemistry", "date": "2001-07-13", "authors": "Hill M M, Andjelkovic M, Brazil D P, Ferrari S, Fabbro D, Hemmings B A", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11373274", "url": "https://glygen.org/publication/PubMed/11373274" } ] }, { "title": "Protein kinase B phosphorylates AHNAK and regulates its subcellular localization.", "journal": "The Journal of cell biology", "date": "2001", "authors": "Sussman J, Stokoe D, Ossina N, Shtivelman E", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11535620", "url": "https://glygen.org/publication/PubMed/11535620" } ] }, { "title": "Inhibition of integrin-linked kinase/protein kinase B/Akt signaling: mechanism for ganglioside-induced apoptosis.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Wang XQ, Sun P, Paller AS", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11577096", "url": "https://glygen.org/publication/PubMed/11577096" } ] }, { "title": "Ganglioside loss promotes survival primarily by activating integrin-linked kinase/Akt without phosphoinositide 3-OH kinase signaling.", "journal": "The Journal of investigative dermatology", "date": "2002", "authors": "Sun P, Wang XQ, Lopatka K, Bangash S, Paller AS", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12164932", "url": "https://glygen.org/publication/PubMed/12164932" } ] }, { "title": "Troglitazone treatment increases protein kinase B phosphorylation in skeletal muscle of normoglycemic subjects at risk for the development of type 2 diabetes.", "journal": "Diabetes", "date": "2002", "authors": "Meyer MM, Levin K, Grimmsmann T, Perwitz N, Eirich A, Beck-Nielsen H, Klein HH", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12196460", "url": "https://glygen.org/publication/PubMed/12196460" } ] }, { "title": "Transforming growth factor-beta1 stimulated protein kinase B serine-473 and focal adhesion kinase tyrosine phosphorylation dependent on cell adhesion in human hepatocellular carcinoma SMMC-7721 cells.", "journal": "Biochemical and biophysical research communications", "date": "2003-12-12", "authors": "Xu Zhen, Ma Dong-zhu, Wang Li-ying, Su Jian-min, Zha Xi-liang", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "14637150", "url": "https://glygen.org/publication/PubMed/14637150" } ] }, { "title": "Glucocorticoids down-regulate glucose uptake capacity and insulin-signaling proteins in omental but not subcutaneous human adipocytes.", "journal": "The Journal of clinical endocrinology and metabolism", "date": "2004", "authors": "Lundgren M, Buren J, Ruge T, Myrnas T, Eriksson JW", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15181089", "url": "https://glygen.org/publication/PubMed/15181089" } ] }, { "title": "[Activation of phosphatidylinositol 3-kinase-protein kinase B (PI3K-PKB) induced by 17beta-estradiol in endometrial carcinoma cell (Ishikawa)].", "journal": "Zhonghua fu chan ke za zhi", "date": "2004", "authors": "Guo RX, Wei LH, Wang JL, Sun PM, Sun XL", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15347471", "url": "https://glygen.org/publication/PubMed/15347471" } ] }, { "title": "Acute activation of Erk1/Erk2 and protein kinase B/akt proceed by independent pathways in multiple cell types.", "journal": "The FEBS journal", "date": "2005", "authors": "Chiu D, Ma K, Scott A, Duronio V", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "16128807", "url": "https://glygen.org/publication/PubMed/16128807" } ] }, { "title": "Preferential dependence of breast cancer cells versus normal cells on integrin-linked kinase for protein kinase B/Akt activation and cell survival.", "journal": "Cancer research", "date": "2006", "authors": "Troussard AA, McDonald PC, Wederell ED, Mawji NM, Filipenko NR, Gelmon KA, Kucab JE, Dunn SE, Emerman JT, Bally MB, Dedhar S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "16397254", "url": "https://glygen.org/publication/PubMed/16397254" } ] }, { "title": "Activation of insulin-like growth factor type-1 receptor is required for H2O2-induced PKB phosphorylation in vascular smooth muscle cells.", "journal": "Canadian journal of physiology and pharmacology", "date": "2006-07", "authors": "Azar Zeina M, Mehdi Mohamad Z, Srivastava Ashok K", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "16998541", "url": "https://glygen.org/publication/PubMed/16998541" } ] }, { "title": "DNA-dependent protein kinase-mediated phosphorylation of protein kinase B requires a specific recognition sequence in the C-terminal hydrophobic motif.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Park J, Feng J, Li Y, Hammarsten O, Brazil DP, Hemmings BA", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19144640", "url": "https://glygen.org/publication/PubMed/19144640" } ] }, { "title": "Regulation of MAP kinase-directed mitogenic and protein kinase B-mediated signaling by cannabinoid receptor type 1 in skeletal muscle cells.", "journal": "Diabetes", "date": "2010-02", "authors": "Lipina Christopher, Stretton Clare, Hastings Simon, Hundal Jonathan S, Mackie Ken, Irving Andrew J, Hundal Harinder S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19933999", "url": "https://glygen.org/publication/PubMed/19933999" } ] }, { "title": "Effects of adrenaline on whole-body glucose metabolism and insulin-mediated regulation of glycogen synthase and PKB phosphorylation in human skeletal muscle.", "journal": "Metabolism: clinical and experimental", "date": "2011", "authors": "Jensen J, Ruge T, Lai YC, Svensson MK, Eriksson JW", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20153492", "url": "https://glygen.org/publication/PubMed/20153492" } ] }, { "title": "A phosphatidylinositol 3-kinase/protein kinase B-independent activation of mammalian target of rapamycin signaling is sufficient to induce skeletal muscle hypertrophy.", "journal": "Molecular biology of the cell", "date": "2010", "authors": "Goodman CA, Miu MH, Frey JW, Mabrey DM, Lincoln HC, Ge Y, Chen J, Hornberger TA", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20668162", "url": "https://glygen.org/publication/PubMed/20668162" } ] }, { "title": "Rapamycin toxicity in MIN6 cells and rat and human islets is mediated by the inhibition of mTOR complex 2 (mTORC2).", "journal": "Diabetologia", "date": "2012-05", "authors": "Barlow A D, Xie J, Moore C E, Campbell S C, Shaw J A M, Nicholson M L, Herbert T P", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "22314813", "url": "https://glygen.org/publication/PubMed/22314813" } ] }, { "title": "12-O-tetradecanoylphorbol-1,3-acetate-induced degradation of protein kinase B via ubiquitin-proteasomal pathway depends on its Ser473 phosphorylation in gastric cancer cells.", "journal": "Folia histochemica et cytobiologica", "date": "2013", "authors": "Zhang Bing, Xia Chun", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "23690212", "url": "https://glygen.org/publication/PubMed/23690212" } ] }, { "title": "Measurement of protein kinase B activity in single primary human pancreatic cancer cells.", "journal": "Analytical chemistry", "date": "2014-05-06", "authors": "Proctor Angela, Herrera-Loeza S Gabriela, Wang Qunzhao, Lawrence David S, Yeh Jen Jen, Allbritton Nancy L", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "24716819", "url": "https://glygen.org/publication/PubMed/24716819" } ] }, { "title": "11\u03b2-HSD1 modulates LPS-induced innate immune responses in adipocytes by altering expression of PTEN.", "journal": "Molecular endocrinology (Baltimore, Md.)", "date": "2015-04", "authors": "Lai Wenfang, Tian Xue, Xiang Qing, Chu Kedan, Wei Yicong, Deng Jingti, Zhang Shaoping, Brown John, Hong Guizhu", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "25734515", "url": "https://glygen.org/publication/PubMed/25734515" } ] }, { "title": "Suppression of phospho-p85alpha-GTP-Rac1 lipid raft interaction by bichalcone analog attenuates cancer cell invasion.", "journal": "Molecular carcinogenesis", "date": "2016", "authors": "Lu HL, Chen SS, Hsu WT, Lu YC, Lee CC, Wu TS, Lin ML", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "26756739", "url": "https://glygen.org/publication/PubMed/26756739" } ] }, { "title": "Cross-talks via mTORC2 can explain enhanced activation in response to insulin in diabetic patients.", "journal": "Bioscience reports", "date": "2017", "authors": "Magnusson R, Gustafsson M, Cedersund G, Stralfors P, Nyman E", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "27986865", "url": "https://glygen.org/publication/PubMed/27986865" } ] }, { "title": "Short-term heat stress altered metabolism and insulin signaling in skeletal muscle.", "journal": "Journal of animal science", "date": "2018-02-15", "authors": "Ganesan Shanthi, Summers Corey M, Pearce Sarah C, Gabler Nicholas K, Valentine Rudy J, Baumgard Lance H, Rhoads Robert P, Selsby Joshua T", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29432553", "url": "https://glygen.org/publication/PubMed/29432553" } ] }, { "title": "Inhibition of Expression of the S100A8 Gene Encoding the S100 Calcium-Binding Protein A8 Promotes Apoptosis by Suppressing the Phosphorylation of Protein Kinase B (Akt) in Endometrial Carcinoma and HEC-1A Cells.", "journal": "Medical science monitor : international medical journal of experimental and clinical research", "date": "2018", "authors": "Liu C, Xing G, Wu C, Zhu J, Wei M, Liu D, Ge Y, Chen Y, Lei T, Yang Y", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29595187", "url": "https://glygen.org/publication/PubMed/29595187" } ] }, { "title": "A newly generated neuronal cell model of CLN7 disease reveals aberrant lysosome motility and impaired cell survival.", "journal": "Molecular genetics and metabolism", "date": "2019", "authors": "von Kleist L, Ariunbat K, Braren I, Stauber T, Storch S, Danyukova T", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "30301600", "url": "https://glygen.org/publication/PubMed/30301600" } ] }, { "title": "Insulin and \u03b2-adrenergic receptors mediate lipolytic and anti-lipolytic signalling that is not altered by type 2 diabetes in human adipocytes.", "journal": "The Biochemical journal", "date": "2019-10-15", "authors": "J\u00f6nsson Cecilia, Castor Batista Ana P, Kj\u00f8lhede Preben, Str\u00e5lfors Peter", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "31519735", "url": "https://glygen.org/publication/PubMed/31519735" } ] }, { "title": "Inner ear is a target for insulin signaling and insulin resistance: evidence from mice and auditory HEI-OC1 cells.", "journal": "BMJ open diabetes research & care", "date": "2020-03", "authors": "P\u00e5lbrink Ann-Ki, Kopietz Franziska, Mor\u00e9n Bj\u00f6rn, In 't Zandt Ren\u00e9, Kalinec Federico, Stenkula Karin, G\u00f6ransson Olga, Holm Cecilia, Magnusson M\u00e5ns, Degerman Eva", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "32238362", "url": "https://glygen.org/publication/PubMed/32238362" } ] }, { "title": "PPAR\u03b4 Attenuates Alcohol-Mediated Insulin Resistance by Enhancing Fatty Acid-Induced Mitochondrial Uncoupling and Antioxidant Defense in Skeletal Muscle.", "journal": "Frontiers in physiology", "date": "2020", "authors": "Koh Jin-Ho, Kim Ki-Hoon, Park Sol-Yi, Kim Yong-Woon, Kim Jong-Yeon", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "32760285", "url": "https://glygen.org/publication/PubMed/32760285" } ] }, { "title": "Melatonin increases growth properties in human dermal papilla spheroids by activating AKT/GSK3\u03b2/\u03b2-Catenin signaling pathway.", "journal": "PeerJ", "date": "2022", "authors": "Bae Sowon, Yoon Yoo Gyeong, Kim Ji Yea, Park In-Chul, An Sungkwan, Lee Jae Ho, Bae Seunghee", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "35607451", "url": "https://glygen.org/publication/PubMed/35607451" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10187855", "url": "https://glygen.org/publication/PubMed/10187855", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10373549", "url": "https://glygen.org/publication/PubMed/10373549", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10385529", "url": "https://glygen.org/publication/PubMed/10385529", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10637513", "url": "https://glygen.org/publication/PubMed/10637513", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10788440", "url": "https://glygen.org/publication/PubMed/10788440", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11373274", "url": "https://glygen.org/publication/PubMed/11373274", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11535620", "url": "https://glygen.org/publication/PubMed/11535620", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11577096", "url": "https://glygen.org/publication/PubMed/11577096", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12164932", "url": "https://glygen.org/publication/PubMed/12164932", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12196460", "url": "https://glygen.org/publication/PubMed/12196460", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14637150", "url": "https://glygen.org/publication/PubMed/14637150", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15181089", "url": "https://glygen.org/publication/PubMed/15181089", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15347471", "url": "https://glygen.org/publication/PubMed/15347471", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16128807", "url": "https://glygen.org/publication/PubMed/16128807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16397254", "url": "https://glygen.org/publication/PubMed/16397254", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16998541", "url": "https://glygen.org/publication/PubMed/16998541", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19144640", "url": "https://glygen.org/publication/PubMed/19144640", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19933999", "url": "https://glygen.org/publication/PubMed/19933999", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20153492", "url": "https://glygen.org/publication/PubMed/20153492", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20668162", "url": "https://glygen.org/publication/PubMed/20668162", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22314813", "url": "https://glygen.org/publication/PubMed/22314813", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23690212", "url": "https://glygen.org/publication/PubMed/23690212", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24716819", "url": "https://glygen.org/publication/PubMed/24716819", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25734515", "url": "https://glygen.org/publication/PubMed/25734515", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26756739", "url": "https://glygen.org/publication/PubMed/26756739", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27986865", "url": "https://glygen.org/publication/PubMed/27986865", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29432553", "url": "https://glygen.org/publication/PubMed/29432553", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29595187", "url": "https://glygen.org/publication/PubMed/29595187", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30301600", "url": "https://glygen.org/publication/PubMed/30301600", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31519735", "url": "https://glygen.org/publication/PubMed/31519735", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32238362", "url": "https://glygen.org/publication/PubMed/32238362", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32760285", "url": "https://glygen.org/publication/PubMed/32760285", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35607451", "url": "https://glygen.org/publication/PubMed/35607451", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NVAVKTCKKDCTLDNKEKFM", "down_seq": "EAVIMKNLDHPHIVKLIGII", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "10187855", "url": "https://glygen.org/publication/PubMed/10187855" }, { "database": "PubMed", "id": "10373549", "url": "https://glygen.org/publication/PubMed/10373549" }, { "database": "PubMed", "id": "10385529", "url": "https://glygen.org/publication/PubMed/10385529" }, { "database": "PubMed", "id": "10637513", "url": "https://glygen.org/publication/PubMed/10637513" }, { "database": "PubMed", "id": "10788440", "url": "https://glygen.org/publication/PubMed/10788440" }, { "database": "PubMed", "id": "11373274", "url": "https://glygen.org/publication/PubMed/11373274" }, { "database": "PubMed", "id": "11535620", "url": "https://glygen.org/publication/PubMed/11535620" }, { "database": "PubMed", "id": "11577096", "url": "https://glygen.org/publication/PubMed/11577096" }, { "database": "PubMed", "id": "12164932", "url": "https://glygen.org/publication/PubMed/12164932" }, { "database": "PubMed", "id": "12196460", "url": "https://glygen.org/publication/PubMed/12196460" }, { "database": "PubMed", "id": "14637150", "url": "https://glygen.org/publication/PubMed/14637150" }, { "database": "PubMed", "id": "15181089", "url": "https://glygen.org/publication/PubMed/15181089" }, { "database": "PubMed", "id": "15347471", "url": "https://glygen.org/publication/PubMed/15347471" }, { "database": "PubMed", "id": "16128807", "url": "https://glygen.org/publication/PubMed/16128807" }, { "database": "PubMed", "id": "16397254", "url": "https://glygen.org/publication/PubMed/16397254" }, { "database": "PubMed", "id": "16998541", "url": "https://glygen.org/publication/PubMed/16998541" }, { "database": "PubMed", "id": "19144640", "url": "https://glygen.org/publication/PubMed/19144640" }, { "database": "PubMed", "id": "19933999", "url": "https://glygen.org/publication/PubMed/19933999" }, { "database": "PubMed", "id": "20153492", "url": "https://glygen.org/publication/PubMed/20153492" }, { "database": "PubMed", "id": "20668162", "url": "https://glygen.org/publication/PubMed/20668162" }, { "database": "PubMed", "id": "22314813", "url": "https://glygen.org/publication/PubMed/22314813" }, { "database": "PubMed", "id": "23690212", "url": "https://glygen.org/publication/PubMed/23690212" }, { "database": "PubMed", "id": "24716819", "url": "https://glygen.org/publication/PubMed/24716819" }, { "database": "PubMed", "id": "25734515", "url": "https://glygen.org/publication/PubMed/25734515" }, { "database": "PubMed", "id": "26756739", "url": "https://glygen.org/publication/PubMed/26756739" }, { "database": "PubMed", "id": "27986865", "url": "https://glygen.org/publication/PubMed/27986865" }, { "database": "PubMed", "id": "29432553", "url": "https://glygen.org/publication/PubMed/29432553" }, { "database": "PubMed", "id": "29595187", "url": "https://glygen.org/publication/PubMed/29595187" }, { "database": "PubMed", "id": "30301600", "url": "https://glygen.org/publication/PubMed/30301600" }, { "database": "PubMed", "id": "31519735", "url": "https://glygen.org/publication/PubMed/31519735" }, { "database": "PubMed", "id": "32238362", "url": "https://glygen.org/publication/PubMed/32238362" }, { "database": "PubMed", "id": "32760285", "url": "https://glygen.org/publication/PubMed/32760285" }, { "database": "PubMed", "id": "35607451", "url": "https://glygen.org/publication/PubMed/35607451" } ], "site_lbl": "Ser473" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14289-1.457.457", "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": 33 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.530.530", "start_pos": 530, "end_pos": 530, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "IEDB", "id": "236187", "url": "https://www.iedb.org/epitope/236187" }, { "database": "IEDB", "id": "441949", "url": "https://www.iedb.org/epitope/441949" }, { "database": "IEDB", "id": "452958", "url": "https://www.iedb.org/epitope/452958" }, { "database": "IEDB", "id": "478018", "url": "https://www.iedb.org/epitope/478018" }, { "database": "IEDB", "id": "576602", "url": "https://www.iedb.org/epitope/576602" }, { "database": "IEDB", "id": "655182", "url": "https://www.iedb.org/epitope/655182" }, { "database": "IEDB", "id": "675804", "url": "https://www.iedb.org/epitope/675804" }, { "database": "IEDB", "id": "779657", "url": "https://www.iedb.org/epitope/779657" }, { "database": "IEDB", "id": "1350239", "url": "https://www.iedb.org/epitope/1350239" }, { "database": "IEDB", "id": "1365504", "url": "https://www.iedb.org/epitope/1365504" }, { "database": "IEDB", "id": "1367441", "url": "https://www.iedb.org/epitope/1367441" }, { "database": "IEDB", "id": "1372288", "url": "https://www.iedb.org/epitope/1372288" }, { "database": "IEDB", "id": "1376980", "url": "https://www.iedb.org/epitope/1376980" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.iedb.org/epitope/Q14289", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGHYLERNKNSLKVLTLVLY", "down_seq": "LQICKAMAYLESINCVHRDI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q14289", "url": "https://www.iedb.org/epitope/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Ser530" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "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": "Q14289-1.579.579", "start_pos": 579, "end_pos": 579, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Inhibition of the catalytic activity of cell adhesion kinase beta by protein-tyrosine phosphatase-PEST-mediated dephosphorylation.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Lyons PD, Dunty JM, Schaefer EM, Schaller MD", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "11337490", "url": "https://glygen.org/publication/PubMed/11337490" } ] }, { "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": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" } ] }, { "title": "HIV-1 gp120 and chemokine activation of Pyk2 and mitogen-activated protein kinases in primary macrophages mediated by calcium-dependent, pertussis toxin-insensitive chemokine receptor signaling.", "journal": "Blood", "date": "2001", "authors": "Del Corno M, Liu QH, Schols D, de Clercq E, Gessani S, Freedman BD, Collman RG", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" } ] }, { "title": "PYK2 autophosphorylation, but not kinase activity, is necessary for adhesion-induced association with c-Src, osteoclast spreading, and bone resorption.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Lakkakorpi PT, Bett AJ, Lipfert L, Rodan GA, Duong LT", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" } ] }, { "title": "Roflumilast inhibits leukocyte-platelet interactions and prevents the prothrombotic functions of polymorphonuclear leukocytes and monocytes.", "journal": "Journal of thrombosis and haemostasis : JTH", "date": "2016", "authors": "Totani L, Amore C, Di Santo A, Dell'Elba G, Piccoli A, Martelli N, Tenor H, Beume R, Evangelista V", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "26484898", "url": "https://glygen.org/publication/PubMed/26484898" } ] }, { "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" } ] }, { "title": "Global Identification of Small Ubiquitin-related Modifier (SUMO) Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration.", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Uzoma I, Hu J, Cox E, Xia S, Zhou J, Rho HS, Guzzo C, Paul C, Ajala O, Goodwin CR, Jeong J, Moore C, Zhang H, Meluh P, Blackshaw S, Matunis M, Qian J, Zhu H", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" } ] }, { "title": "Proline-rich tyrosine kinase 2 mediates transforming growth factor-beta-induced hepatic stellate cell activation and liver fibrosis.", "journal": "Scientific reports", "date": "2020-12-03", "authors": "Kim Jonghwa, Kang Wonseok, Kang So Hee, Park Su Hyun, Kim Ji Young, Yang Sera, Ha Sang Yun, Paik Yong-Han", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11337490", "url": "https://glygen.org/publication/PubMed/11337490", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289", "database": "PRO", "categories": [ "Other" ] }, { "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26484898", "url": "https://glygen.org/publication/PubMed/26484898", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SPECVKLGDFGLSRYIEDED", "down_seq": "YKASVTRLPIKWMSPESINF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q14289-1", "kinase_gene_name": "PTK2B", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "11337490", "url": "https://glygen.org/publication/PubMed/11337490" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" } ], "site_lbl": "Tyr579" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PRO", "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" }, { "database": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" }, { "database": "PubMed", "id": "26484898", "url": "https://glygen.org/publication/PubMed/26484898" }, { "database": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" }, { "database": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" }, { "database": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" } ], "site_lbl": "Tyr579" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q14289-1.580.580", "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": 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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.580.580", "start_pos": 580, "end_pos": 580, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Inhibition of the catalytic activity of cell adhesion kinase beta by protein-tyrosine phosphatase-PEST-mediated dephosphorylation.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Lyons PD, Dunty JM, Schaefer EM, Schaller MD", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "11337490", "url": "https://glygen.org/publication/PubMed/11337490" } ] }, { "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": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "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": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" } ] }, { "title": "HIV-1 gp120 and chemokine activation of Pyk2 and mitogen-activated protein kinases in primary macrophages mediated by calcium-dependent, pertussis toxin-insensitive chemokine receptor signaling.", "journal": "Blood", "date": "2001", "authors": "Del Corno M, Liu QH, Schols D, de Clercq E, Gessani S, Freedman BD, Collman RG", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" } ] }, { "title": "Protein-tyrosine kinase Pyk2 is involved in interleukin-2 production by Jurkat T cells via its tyrosine 402.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Katagiri T, Takahashi T, Sasaki T, Nakamura S, Hattori S", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021" } ] }, { "title": "Human endothelial Pyk2 is expressed in two isoforms and associates with paxillin and p130Cas.", "journal": "Biochemical and biophysical research communications", "date": "2002", "authors": "Keogh RJ, Houliston RA, Wheeler-Jones CP", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787" } ] }, { "title": "PYK2 autophosphorylation, but not kinase activity, is necessary for adhesion-induced association with c-Src, osteoclast spreading, and bone resorption.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Lakkakorpi PT, Bett AJ, Lipfert L, Rodan GA, Duong LT", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" } ] }, { "title": "The epidermal growth factor receptor (EGFR) and proline rich tyrosine kinase 2 (PYK2) are involved in tissue factor dependent factor VIIa signalling in HaCaT cells.", "journal": "Thrombosis and haemostasis", "date": "2004", "authors": "Wiiger MT, Prydz H", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15213840", "url": "https://glygen.org/publication/PubMed/15213840" } ] }, { "title": "Ephrin-A1 binding to CD4+ T lymphocytes stimulates migration and induces tyrosine phosphorylation of PYK2.", "journal": "Blood", "date": "2005", "authors": "Aasheim HC, Delabie J, Finne EF", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "15585656", "url": "https://glygen.org/publication/PubMed/15585656" } ] }, { "title": "Differential regulation of Pyk2 phosphorylation at Tyr-402 and Tyr-580 in intestinal epithelial cells: roles of calcium, Src, Rho kinase, and the cytoskeleton.", "journal": "Cellular signalling", "date": "2006", "authors": "Wu SS, Jacamo RO, Vong SK, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "16574377", "url": "https://glygen.org/publication/PubMed/16574377" } ] }, { "title": "Survival response-linked Pyk2 activation during potassium depletion-induced apoptosis of cerebellar granule neurons.", "journal": "Molecular and cellular neurosciences", "date": "2007", "authors": "Strappazzon F, Torch S, Trioulier Y, Blot B, Sadoul R, Verna JM", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "17188509", "url": "https://glygen.org/publication/PubMed/17188509" } ] }, { "title": "Comparison of T cell receptor-induced proximal signaling and downstream functions in immortalized and primary T cells.", "journal": "PloS one", "date": "2009", "authors": "Bartelt RR, Cruz-Orcutt N, Collins M, Houtman JC", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19412549", "url": "https://glygen.org/publication/PubMed/19412549" } ] }, { "title": "The T cell receptor-mediated phosphorylation of Pyk2 tyrosines 402 and 580 occurs via a distinct mechanism than other receptor systems.", "journal": "Journal of leukocyte biology", "date": "2010", "authors": "Collins M, Tremblay M, Chapman N, Curtiss M, Rothman PB, Houtman JC", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20028775", "url": "https://glygen.org/publication/PubMed/20028775" } ] }, { "title": "T cell receptor activation leads to two distinct phases of Pyk2 activation and actin cytoskeletal rearrangement in human T cells.", "journal": "Molecular immunology", "date": "2010", "authors": "Collins M, Bartelt RR, Houtman JC", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "20381867", "url": "https://glygen.org/publication/PubMed/20381867" } ] }, { "title": "Non-catalytic functions of Pyk2 and Fyn regulate late stage adhesion in human T cells.", "journal": "PloS one", "date": "2012", "authors": "Chapman NM, Yoder AN, Houtman JC", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "23300847", "url": "https://glygen.org/publication/PubMed/23300847" } ] }, { "title": "Roflumilast inhibits leukocyte-platelet interactions and prevents the prothrombotic functions of polymorphonuclear leukocytes and monocytes.", "journal": "Journal of thrombosis and haemostasis : JTH", "date": "2016", "authors": "Totani L, Amore C, Di Santo A, Dell'Elba G, Piccoli A, Martelli N, Tenor H, Beume R, Evangelista V", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "26484898", "url": "https://glygen.org/publication/PubMed/26484898" } ] }, { "title": "Global Identification of Small Ubiquitin-related Modifier (SUMO) Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration.", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Uzoma I, Hu J, Cox E, Xia S, Zhou J, Rho HS, Guzzo C, Paul C, Ajala O, Goodwin CR, Jeong J, Moore C, Zhang H, Meluh P, Blackshaw S, Matunis M, Qian J, Zhu H", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" } ] }, { "title": "Proline-rich tyrosine kinase 2 mediates transforming growth factor-beta-induced hepatic stellate cell activation and liver fibrosis.", "journal": "Scientific reports", "date": "2020-12-03", "authors": "Kim Jonghwa, Kang Wonseok, Kang So Hee, Park Su Hyun, Kim Ji Young, Yang Sera, Ha Sang Yun, Paik Yong-Han", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11337490", "url": "https://glygen.org/publication/PubMed/11337490", "database": "PubMed", "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289", "database": "PRO", "categories": [ "Other" ] }, { "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15213840", "url": "https://glygen.org/publication/PubMed/15213840", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15585656", "url": "https://glygen.org/publication/PubMed/15585656", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16574377", "url": "https://glygen.org/publication/PubMed/16574377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17188509", "url": "https://glygen.org/publication/PubMed/17188509", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19412549", "url": "https://glygen.org/publication/PubMed/19412549", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20028775", "url": "https://glygen.org/publication/PubMed/20028775", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20381867", "url": "https://glygen.org/publication/PubMed/20381867", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23300847", "url": "https://glygen.org/publication/PubMed/23300847", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26484898", "url": "https://glygen.org/publication/PubMed/26484898", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PECVKLGDFGLSRYIEDEDY", "down_seq": "KASVTRLPIKWMSPESINFR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q14289-1", "kinase_gene_name": "PTK2B", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "11337490", "url": "https://glygen.org/publication/PubMed/11337490" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" } ], "site_lbl": "Tyr580" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by SRC, FYN and LCK", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PRO", "id": "Q14289", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "11698270", "url": "https://glygen.org/publication/PubMed/11698270" }, { "database": "PubMed", "id": "10867021", "url": "https://glygen.org/publication/PubMed/10867021" }, { "database": "PubMed", "id": "11820787", "url": "https://glygen.org/publication/PubMed/11820787" }, { "database": "PubMed", "id": "12514172", "url": "https://glygen.org/publication/PubMed/12514172" }, { "database": "PubMed", "id": "15213840", "url": "https://glygen.org/publication/PubMed/15213840" }, { "database": "PubMed", "id": "15585656", "url": "https://glygen.org/publication/PubMed/15585656" }, { "database": "PubMed", "id": "16574377", "url": "https://glygen.org/publication/PubMed/16574377" }, { "database": "PubMed", "id": "17188509", "url": "https://glygen.org/publication/PubMed/17188509" }, { "database": "PubMed", "id": "19412549", "url": "https://glygen.org/publication/PubMed/19412549" }, { "database": "PubMed", "id": "20028775", "url": "https://glygen.org/publication/PubMed/20028775" }, { "database": "PubMed", "id": "20381867", "url": "https://glygen.org/publication/PubMed/20381867" }, { "database": "PubMed", "id": "23300847", "url": "https://glygen.org/publication/PubMed/23300847" }, { "database": "PubMed", "id": "26484898", "url": "https://glygen.org/publication/PubMed/26484898" }, { "database": "PubMed", "id": "29438996", "url": "https://glygen.org/publication/PubMed/29438996" }, { "database": "PubMed", "id": "33273492", "url": "https://glygen.org/publication/PubMed/33273492" } ], "site_lbl": "Tyr580" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q14289-1.579.579", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 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": 18 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.722.722", "start_pos": 722, "end_pos": 722, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PKILEPTAFQEPPPKPSRPK", "down_seq": "RPPPQTNLLAPKLQFQVPEG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Tyr722" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "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": "Q14289-1.756.756", "start_pos": 756, "end_pos": 756, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QFQVPEGLCASSPTLTSPME", "down_seq": "PSPVNSLHTPPLHRHNVFKR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Tyr756" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q14289-1.758.758", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14289-1.762.762", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14289-1.765.765", "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": "Q14289-1.758.758", "start_pos": 758, "end_pos": 758, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "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": "QVPEGLCASSPTLTSPMEYP", "down_seq": "PVNSLHTPPLHRHNVFKRHS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser758" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q14289-1.756.756", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14289-1.762.762", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14289-1.765.765", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14289-1.778.778", "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": "Q14289-1.762.762", "start_pos": 762, "end_pos": 762, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "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": "GLCASSPTLTSPMEYPSPVN", "down_seq": "LHTPPLHRHNVFKRHSMREE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser762" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q14289-1.756.756", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14289-1.758.758", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14289-1.765.765", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14289-1.778.778", "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": "Q14289-1.765.765", "start_pos": 765, "end_pos": 765, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ASSPTLTSPMEYPSPVNSLH", "down_seq": "PPLHRHNVFKRHSMREEDFI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Thr765" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q14289-1.756.756", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14289-1.758.758", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14289-1.762.762", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14289-1.778.778", "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": "Q14289-1.778.778", "start_pos": 778, "end_pos": 778, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" } ] }, { "title": "Pyk2 cytonuclear localization: mechanisms and regulation by serine dephosphorylation.", "journal": "Cellular and molecular life sciences : CMLS", "date": "2013", "authors": "Faure C, Ramos M, Girault JA", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "22802128", "url": "https://glygen.org/publication/PubMed/22802128" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22802128", "url": "https://glygen.org/publication/PubMed/22802128", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPVNSLHTPPLHRHNVFKRH", "down_seq": "MREEDFIQPSSREEAQQLWE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q14289-1", "kinase_gene_name": "PTK2B", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" } ], "site_lbl": "Ser778" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "22802128", "url": "https://glygen.org/publication/PubMed/22802128" } ], "site_lbl": "Ser778" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14289-1.758.758", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q14289-1.762.762", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14289-1.765.765", "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": "Q14289-1.819.819", "start_pos": 819, "end_pos": 819, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AEKVKMRQILDKQQKQMVED", "down_seq": "QWLRQEEKSLDPMVYMNDKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Tyr819" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14289-1.805.805", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14289-1.834.834", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14289-1.839.839", "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": "Q14289-1.834.834", "start_pos": 834, "end_pos": 834, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QMVEDYQWLRQEEKSLDPMV", "down_seq": "MNDKSPLTPEKEVGYLEFTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Tyr834" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14289-1.819.819", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14289-1.839.839", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14289-1.842.842", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14289-1.849.849", "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": "Q14289-1.839.839", "start_pos": 839, "end_pos": 839, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "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": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YQWLRQEEKSLDPMVYMNDK", "down_seq": "PLTPEKEVGYLEFTGPPQKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Ser839" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14289-1.819.819", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14289-1.834.834", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14289-1.842.842", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14289-1.849.849", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14289-1.859.859", "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": "Q14289-1.842.842", "start_pos": 842, "end_pos": 842, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LRQEEKSLDPMVYMNDKSPL", "down_seq": "PEKEVGYLEFTGPPQKPPRL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Thr842" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14289-1.834.834", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14289-1.839.839", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14289-1.849.849", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14289-1.859.859", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14289-1.849.849", "start_pos": 849, "end_pos": 849, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LDPMVYMNDKSPLTPEKEVG", "down_seq": "LEFTGPPQKPPRLGAQSIQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Tyr849" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14289-1.834.834", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14289-1.839.839", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14289-1.842.842", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14289-1.859.859", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14289-1.864.864", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14289-1.866.866", "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": "Q14289-1.866.866", "start_pos": 866, "end_pos": 866, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "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": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EVGYLEFTGPPQKPPRLGAQ", "down_seq": "IQPTANLDRTDDLVYLNVME", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "site_lbl": "Ser866" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14289-1.849.849", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14289-1.859.859", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14289-1.864.864", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14289-1.881.881", "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": "Q14289-1.906.906", "start_pos": 906, "end_pos": 906, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "SHP2 mediates the protective effect of interleukin-6 against dexamethasone-induced apoptosis in multiple myeloma cells.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Chauhan D, Pandey P, Hideshima T, Treon S, Raje N, Davies FE, Shima Y, Tai YT, Rosen S, Avraham S, Kharbanda S, Anderson KC", "evidence": [ { "database": "iPTMnet", "id": "Q14289-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289-1" } ], "reference": [ { "type": "PubMed", "id": "10880513", "url": "https://glygen.org/publication/PubMed/10880513" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10880513", "url": "https://glygen.org/publication/PubMed/10880513", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ELVRAVLELKNELCQLPPEG", "down_seq": "VVVVKNVGLTLRKLIGSVDD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q06124-2", "kinase_gene_name": "PTPN11", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "10880513", "url": "https://glygen.org/publication/PubMed/10880513" } ], "site_lbl": "Tyr906" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14289-1.889.889", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14289-1.893.893", "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": "Q14289-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "Q14289-1", "length": 1009, "uniprot_id": "FAK2_HUMAN", "protein_name": "Protein-tyrosine kinase 2-beta", "refseq_ac": "NP_004094", "refseq_name": "protein-tyrosine kinase 2-beta isoform a", "gene_name": "PTK2B", "gene_names_uniprotkb": "PTK2B; FAK2; PYK2; RAFTK", "gene_names_refseq": "CADTK; CAKB; FADK2; FAK2; PKB; PTK2B; PTK; PYK2; RAFTK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14289", "url": "https://www.uniprot.org/uniprotkb/Q14289" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Melatonin increases growth properties in human dermal papilla spheroids by activating AKT/GSK3\u03b2/\u03b2-Catenin signaling pathway.", "journal": "PeerJ", "date": "2022", "authors": "Bae Sowon, Yoon Yoo Gyeong, Kim Ji Yea, Park In-Chul, An Sungkwan, Lee Jae Ho, Bae Seunghee", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "35607451", "url": "https://glygen.org/publication/PubMed/35607451" } ] }, { "title": "Essential role for protein kinase B (PKB) in insulin-induced glycogen synthase kinase 3 inactivation. Characterization of dominant-negative mutant of PKB.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "van Weeren PC, de Bruyn KM, de Vries-Smits AM, van Lint J, Burgering BM", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" } ], "reference": [ { "type": "PubMed", "id": "9582355", "url": "https://glygen.org/publication/PubMed/9582355" } ] } ], "crossref": [ { "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "35607451", "url": "https://glygen.org/publication/PubMed/35607451", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9582355", "url": "https://glygen.org/publication/PubMed/9582355", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSGVSEPL", "down_seq": "RVKLGTLRRPEGPAEPMVVV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14289", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14289" }, { "database": "PubMed", "id": "35607451", "url": "https://glygen.org/publication/PubMed/35607451" }, { "database": "PubMed", "id": "9582355", "url": "https://glygen.org/publication/PubMed/9582355" } ], "site_lbl": "Ser9" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "859", "end_pos": "859" }, { "start_pos": "881", "end_pos": "881" } ] }, { "type": "snv", "site_list": [ { "start_pos": "134", "end_pos": "134" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "889", "end_pos": "889" }, { "start_pos": "893", "end_pos": "893" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "361", "end_pos": "361" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "762", "end_pos": "762" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "778", "end_pos": "778" }, { "start_pos": "819", "end_pos": "819" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q14289-1.0.0", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6UWH4-1.133.157", "start_pos": 133, "end_pos": 157, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "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": "HAVASAAPGQEALVGPSLQPQEAAR", "start_aa": "H", "up_seq": "SKRSKPANIRGTVKPKRRKK", "down_seq": "EADAVAPGYAQGANLVKIGE", "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": "HAVASAAPGQEALVGPSLQPQEAAR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "His", "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": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6UWH4-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6UWH4-1.137.137", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6UWH4-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6UWH4-1.149.149", "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": "Q6UWH4-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "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" } ] }, { "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": "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": "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": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs960814724", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs960814724", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs960814724", "url": "https://www.ncbi.nlm.nih.gov/snp/rs960814724#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs960814724", "url": "http://gnomad.broadinstitute.org/awesome?query=rs960814724", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPANIRGTVKPKRRKKHAVA", "down_seq": "AAPGQEALVGPSLQPQEAAR", "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": "Ser137", "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": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" }, { "id": "rs960814724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs960814724" }, { "id": "rs960814724", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs960814724#frequency_tab" }, { "id": "rs960814724", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs960814724" } ], "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": "4", "chr_pos": "158170966", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S137", "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": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6UWH4-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "downstream", "id": "Q6UWH4-1.133.157", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6UWH4-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6UWH4-1.149.149", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6UWH4-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "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": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs371816850", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371816850", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371816850", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371816850", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371816850", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371816850#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371816850", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371816850", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRKKHAVASAAPGQEALVGP", "down_seq": "LQPQEAAREADAVAPGYAQG", "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": "Ser149", "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": "S", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser149", "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": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "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": "4", "chr_pos": "158170930", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S149", "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": "rs371816850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371816850" }, { "id": "rs371816850", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371816850" }, { "id": "rs371816850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371816850#frequency_tab" }, { "id": "rs371816850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371816850" } ], "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": "4", "chr_pos": "158170931", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S149", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6UWH4-1.133.157", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6UWH4-1.137.137", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6UWH4-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6UWH4-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KQPLDMSEVFAFHLDRILGL", "down_seq": "RTLPSVSRKAEFIQDGRPCP", "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": "Asn289", "evidence": [ { "id": "Q6UWH4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q6UWH4-1.291.291", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs772179552", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179552", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772179552", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179552", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772179552", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772179552#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772179552", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772179552", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs772179552", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772179552", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQPNVVYITLRSKRSKPANI", "down_seq": "GTVKPKRRKKHAVASAAPGQ", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" }, { "id": "rs772179552", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179552" }, { "id": "rs772179552", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179552" }, { "id": "rs772179552", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772179552#frequency_tab" }, { "id": "rs772179552", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772179552" }, { "id": "rs772179552", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772179552" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIR->NIC).", "chr_id": "4", "chr_pos": "158171012", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R122", "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": "rs772179552", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179552" }, { "id": "rs772179552", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179552" }, { "id": "rs772179552", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772179552#frequency_tab" }, { "id": "rs772179552", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772179552" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIR->NIS).", "chr_id": "4", "chr_pos": "158171012", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R122", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q6UWH4-1.133.157", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6UWH4-1.137.137", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "Q6UWH4-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VKPKRRKKHAVASAAPGQEA", "down_seq": "VGPSLQPQEAAREADAVAPG", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "L", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "158170942", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L145", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6UWH4-1.133.157", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6UWH4-1.137.137", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6UWH4-1.149.149", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1451179816", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451179816", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1451179816", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451179816", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MTCPDKPGQLINW", "down_seq": "ICSLCVPRVRKLWSSRRPRT", "snv": [ { "evidence": [ { "id": "rs1451179816", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451179816" }, { "id": "rs1451179816", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451179816" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NWF->NWC).", "chr_id": "4", "chr_pos": "158171335", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F14", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q6UWH4-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6UWH4-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6UWH4-1.28.28", "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": "Q6UWH4-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751681878", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751681878", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751681878", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751681878", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751681878", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751681878", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RAGGPDFLQPSSRESNIRIY", "down_seq": "ESAPSWLSKDDIRRMRLLAD", "snv": [ { "evidence": [ { "id": "rs751681878", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751681878" }, { "id": "rs751681878", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751681878" }, { "id": "rs751681878", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751681878" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SES->NES).", "chr_id": "4", "chr_pos": "158170750", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S209", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6UWH4-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AGGPDFLQPSSRESNIRIYS", "down_seq": "SAPSWLSKDDIRRMRLLADS", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "158170748", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E210", "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": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6UWH4-1.209.209", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TCPDKPGQLINWFICSLCVP", "down_seq": "VRKLWSSRRPRTRRNLLLGT", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "158171311", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R22", "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": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6UWH4-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6UWH4-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6UWH4-1.28.28", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PDKPGQLINWFICSLCVPRV", "down_seq": "KLWSSRRPRTRRNLLLGTAC", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "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": "4", "chr_pos": "158171305", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R24", "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: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": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6UWH4-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6UWH4-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6UWH4-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6UWH4-1.43.43", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GQLINWFICSLCVPRVRKLW", "down_seq": "SRRPRTRRNLLLGTACAIYL", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "158171293", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S28", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6UWH4-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6UWH4-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6UWH4-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6UWH4-1.43.43", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q6UWH4-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PLDMSEVFAFHLDRILGLNR", "down_seq": "LPSVSRKAEFIQDGRPCPII", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NRT->NRI).", "chr_id": "4", "chr_pos": "158170504", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T291", "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": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6UWH4-1.289.289", "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": "Q6UWH4-1.380.380", "start_pos": 380, "end_pos": 380, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1452397937", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452397937", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1452397937", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1452397937#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "HHHEWSKMALFDFLLQIYNR", "down_seq": "DTNCCGFRPRKEDACVQNGL", "snv": [ { "evidence": [ { "id": "rs1452397937", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452397937" }, { "id": "rs1452397937", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1452397937#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRL->NRS).", "chr_id": "4", "chr_pos": "158130999", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L380", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q6UWH4-1.400.400", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765768597", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765768597", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765768597", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765768597", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765768597", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765768597", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LDTNCCGFRPRKEDACVQNG", "down_seq": "RPKCDDQGSAALAHIIQRKH", "snv": [ { "evidence": [ { "id": "rs765768597", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765768597" }, { "id": "rs765768597", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765768597" }, { "id": "rs765768597", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765768597" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGL->NGS).", "chr_id": "4", "chr_pos": "158130939", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L400", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6UWH4-1.380.380", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs17857283", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17857283", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs17857283", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17857283", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs17857283", "url": "https://www.ncbi.nlm.nih.gov/snp/rs17857283#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs17857283", "url": "http://gnomad.broadinstitute.org/awesome?query=rs17857283", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs17857283", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs17857283", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LAHIIQRKHDPRHLVFIDNK", "down_seq": "FFDRSEDNLNFKLLEGIKEF", "snv": [ { "evidence": [ { "id": "rs17857283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17857283" }, { "id": "rs17857283", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17857283" }, { "id": "rs17857283", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs17857283#frequency_tab" }, { "id": "rs17857283", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs17857283" }, { "id": "rs17857283", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs17857283" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKG->NKC).", "chr_id": "4", "chr_pos": "158130844", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G432", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs17857283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17857283" }, { "id": "rs17857283", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17857283" }, { "id": "rs17857283", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs17857283#frequency_tab" }, { "id": "rs17857283", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs17857283" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKG->NKS).", "chr_id": "4", "chr_pos": "158130844", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G432", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q6UWH4-1.442.442", "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": 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": "Q6UWH4-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6UWH4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VRKLWSSRRPRTRRNLLLGT", "down_seq": "CAIYLGFLVSQVGRASLQHG", "snv": [ { "evidence": [ { "id": "Q6UWH4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6UWH4" } ], "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": "4", "chr_pos": "158171248", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A43", "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": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6UWH4-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q6UWH4-1.28.28", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6UWH4-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "Q6UWH4-1", "length": 519, "uniprot_id": "GAK1B_HUMAN", "protein_name": "Golgi-associated kinase 1B", "refseq_ac": "NP_001026870", "refseq_name": "Golgi-associated kinase 1B isoform 1", "gene_name": "GASK1B", "gene_names_uniprotkb": "GASK1B; AD021; C4orf18; ENED; FAM198B; PRO6001", "gene_names_refseq": "AD021; AD036; C4orf18; ENED; FAM198B; GASK1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6UWH4", "url": "https://www.uniprot.org/uniprotkb/Q6UWH4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1730647087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1730647087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1730647087", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1730647087#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PRHLVFIDNKGFFDRSEDNL", "down_seq": "FKLLEGIKEFPASAVSVLKS", "snv": [ { "evidence": [ { "id": "rs1730647087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1730647087" }, { "id": "rs1730647087", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1730647087#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLN->NLS).", "chr_id": "4", "chr_pos": "158130813", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N442", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "133", "end_pos": "157" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "289", "end_pos": "289" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6UWH4-1.432.432", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P24592-1.109.134", "start_pos": 109, "end_pos": 134, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "APAVAEENPKESKPQAGTARPQDVNR", "start_aa": "A", "up_seq": "DDEAPLRALLLGRGRCLPAR", "down_seq": "RDQQRNPGTSTTPSQPNSAG", "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": "APAVAEENPKESKPQAGTARPQDVNR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ala", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P24592-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P24592-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P24592-1.153.153", "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": "P24592-1.109.135", "start_pos": 109, "end_pos": 135, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "APAVAEENPKESKPQAGTARPQDVNRR", "start_aa": "A", "up_seq": "DDEAPLRALLLGRGRCLPAR", "down_seq": "DQQRNPGTSTTPSQPNSAGV", "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": "APAVAEENPKESKPQAGTARPQDVNRR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ala", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "P24592-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P24592-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P24592-1.153.153", "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": "P24592-1.119.134", "start_pos": 119, "end_pos": 134, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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" } ] }, { "title": "Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy.", "journal": "Analytical chemistry", "date": "2017", "authors": "Qin H, Cheng K, Zhu J, Mao J, Wang F, Dong M, Chen R, Guo Z, Liang X, Ye M, Zou H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "28035807", "url": "https://glygen.org/publication/PubMed/28035807" } ] }, { "title": "Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy", "journal": "Anal. Chem.", "date": "2017", "authors": "Qin H., Cheng K., Zhu J., Mao J., Wang F., Dong M., Chen R., Guo Z., Liang X., Ye M., Zou H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1021/acs.analchem.6b02887", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "28035807", "url": "https://glygen.org/publication/PubMed/28035807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1021/acs.analchem.6b02887", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887", "database": "DOI", "categories": [ "Other" ] } ], "site_seq": "ESKPQAGTARPQDVNR", "start_aa": "E", "up_seq": "LGRGRCLPARAPAVAEENPK", "down_seq": "RDQQRNPGTSTTPSQPNSAG", "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": "ESKPQAGTARPQDVNR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Glu", "end_aa": "Arg", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" }, { "id": "28035807", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28035807" }, { "id": "10.1021/acs.analchem.6b02887", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P24592-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P24592-1.153.153", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.119.135", "start_pos": 119, "end_pos": 135, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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" } ] }, { "title": "Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy.", "journal": "Analytical chemistry", "date": "2017", "authors": "Qin H, Cheng K, Zhu J, Mao J, Wang F, Dong M, Chen R, Guo Z, Liang X, Ye M, Zou H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "28035807", "url": "https://glygen.org/publication/PubMed/28035807" } ] }, { "title": "Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy", "journal": "Anal. Chem.", "date": "2017", "authors": "Qin H., Cheng K., Zhu J., Mao J., Wang F., Dong M., Chen R., Guo Z., Liang X., Ye M., Zou H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1021/acs.analchem.6b02887", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "28035807", "url": "https://glygen.org/publication/PubMed/28035807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1021/acs.analchem.6b02887", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887", "database": "DOI", "categories": [ "Other" ] } ], "site_seq": "ESKPQAGTARPQDVNRR", "start_aa": "E", "up_seq": "LGRGRCLPARAPAVAEENPK", "down_seq": "DQQRNPGTSTTPSQPNSAGV", "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": "ESKPQAGTARPQDVNRR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Glu", "end_aa": "Arg", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" }, { "id": "28035807", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28035807" }, { "id": "10.1021/acs.analchem.6b02887", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P24592-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P24592-1.153.153", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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" } ] }, { "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": "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": "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": "rs1355880327", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355880327", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1355880327", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355880327", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GRGRCLPARAPAVAEENPKE", "down_seq": "KPQAGTARPQDVNRRDQQRN", "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": "Ser120", "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": "rs1355880327", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355880327" }, { "id": "rs1355880327", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355880327" } ], "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": "12", "chr_pos": "53100736", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S120", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P24592-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "Site-specific O-Glycosylation Analysis of Human Blood Plasma Proteins.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Hoffmann M, Marx K, Reichl U, Wuhrer M, Rapp E", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "26598643", "url": "https://glygen.org/publication/PubMed/26598643" } ] }, { "title": "LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins.", "journal": "Journal of proteome research", "date": "2013", "authors": "Halim A, Ruetschi U, Larson G, Nilsson J", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "656", "url": "https://glyconnect.expasy.org/browser/proteins/656" } ], "reference": [ { "type": "PubMed", "id": "23234360", "url": "https://glygen.org/publication/PubMed/23234360" } ] }, { "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": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" }, { "database": "GlyConnect", "id": "656", "url": "https://glyconnect.expasy.org/browser/proteins/656" } ], "reference": [ { "type": "PubMed", "id": "19838169", "url": "https://glygen.org/publication/PubMed/19838169" } ] }, { "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" } ] }, { "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": "656", "url": "https://glyconnect.expasy.org/browser/proteins/656" } ], "reference": [ { "type": "PubMed", "id": "30237853", "url": "https://glygen.org/publication/PubMed/30237853" } ] }, { "title": "Identification of O-glycosylation sites and partial characterization of carbohydrate structure and disulfide linkages of human insulin-like growth factor binding protein 6.", "journal": "Biochemistry", "date": "1998", "authors": "Neumann GM, Marinaro JA, Bach LA", "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" }, { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875" } ] } ], "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": "26598643", "url": "https://glygen.org/publication/PubMed/26598643", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23234360", "url": "https://glygen.org/publication/PubMed/23234360", "database": "PubMed", "categories": [ "Other" ] }, { "id": "656", "url": "https://glyconnect.expasy.org/browser/proteins/656", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "19838169", "url": "https://glygen.org/publication/PubMed/19838169", "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": "30237853", "url": "https://glygen.org/publication/PubMed/30237853", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PARAPAVAEENPKESKPQAG", "down_seq": "ARPQDVNRRDQQRNPGTSTT", "glycosylation": [ { "glytoucan_ac": "G17015OC", "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": "Thr126", "evidence": [ { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "26598643", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26598643" } ] }, { "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": "Thr126", "evidence": [ { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "26598643", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26598643" } ] }, { "glytoucan_ac": "G29931IJ", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr126", "evidence": [ { "id": "23234360", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23234360" }, { "id": "656", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/656" }, { "id": "19838169", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19838169" } ] }, { "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": "Thr126", "evidence": [ { "id": "23234360", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23234360" }, { "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": "Thr126", "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": "G81006GJ", "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": "Thr126", "evidence": [ { "id": "30237853", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30237853" }, { "id": "656", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/656" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "Other", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true, "automatic_literature_mining": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (HexNAc...) threonine;Other", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr126", "evidence": [ { "id": "P24592", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "id": "19838169", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19838169" }, { "id": "9572875", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9572875" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P24592-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P24592-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 6 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 6 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.140.164", "start_pos": 140, "end_pos": 164, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "NPGTSTTPSQPNSAGVQDTEMGPCR", "start_aa": "N", "up_seq": "SKPQAGTARPQDVNRRDQQR", "down_seq": "RHLDSVLQQLQTEVYRGAQT", "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": "NPGTSTTPSQPNSAGVQDTEMGPCR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Asn", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P24592-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P24592-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P24592-1.166.180", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P24592-1.176.176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P24592-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P24592-1.181.193", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P24592-1.184.184", "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" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 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": "P24592-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "rs760115536", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760115536", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760115536", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760115536#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760115536", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760115536", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1937813590", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1937813590", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1937813590", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1937813590#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QAGTARPQDVNRRDQQRNPG", "down_seq": "STTPSQPNSAGVQDTEMGPC", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr143", "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": "rs760115536", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536" }, { "id": "rs760115536", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536" }, { "id": "rs760115536", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760115536#frequency_tab" }, { "id": "rs760115536", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760115536" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "12", "chr_pos": "53100811", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T143", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1937813590", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1937813590" }, { "id": "rs1937813590", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1937813590#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "12", "chr_pos": "53100804", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T143", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P24592-1.153.153", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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" } ] }, { "title": "Identification of O-glycosylation sites and partial characterization of carbohydrate structure and disulfide linkages of human insulin-like growth factor binding protein 6.", "journal": "Biochemistry", "date": "1998", "authors": "Neumann GM, Marinaro JA, Bach LA", "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" }, { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875" } ] } ], "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": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs201621853", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201621853", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201621853", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201621853", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201621853", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201621853#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201621853", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201621853", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AGTARPQDVNRRDQQRNPGT", "down_seq": "TTPSQPNSAGVQDTEMGPCR", "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": "Ser144", "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" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "Other", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true, "automatic_literature_mining": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (HexNAc...) serine;Other", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser144", "evidence": [ { "id": "P24592", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "id": "9572875", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9572875" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "snv": [ { "evidence": [ { "id": "rs201621853", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201621853" }, { "id": "rs201621853", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201621853" }, { "id": "rs201621853", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201621853#frequency_tab" }, { "id": "rs201621853", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201621853" } ], "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": "53100807", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.153.153", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "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", "mining_tool" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P24592-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "Identification of O-glycosylation sites and partial characterization of carbohydrate structure and disulfide linkages of human insulin-like growth factor binding protein 6.", "journal": "Biochemistry", "date": "1998", "authors": "Neumann GM, Marinaro JA, Bach LA", "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" }, { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875" } ] } ], "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": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs760115536", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760115536", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760115536", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760115536#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760115536", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760115536", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GTARPQDVNRRDQQRNPGTS", "down_seq": "TPSQPNSAGVQDTEMGPCRR", "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": "Thr145", "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": "Thr145", "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": "Thr145", "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" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "Other", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true, "automatic_literature_mining": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (HexNAc...) threonine;Other", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr145", "evidence": [ { "id": "P24592", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "id": "9572875", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9572875" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "snv": [ { "evidence": [ { "id": "rs760115536", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536" }, { "id": "rs760115536", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760115536" }, { "id": "rs760115536", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760115536#frequency_tab" }, { "id": "rs760115536", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760115536" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "12", "chr_pos": "53100811", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.153.153", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "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", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "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", "mining_tool" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P24592-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "Identification of O-glycosylation sites and partial characterization of carbohydrate structure and disulfide linkages of human insulin-like growth factor binding protein 6.", "journal": "Biochemistry", "date": "1998", "authors": "Neumann GM, Marinaro JA, Bach LA", "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" }, { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875" } ] } ], "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": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs765946180", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765946180", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765946180", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765946180", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765946180", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765946180#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765946180", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765946180", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs765946180", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765946180", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1212727893", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1212727893", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1212727893", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1212727893", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TARPQDVNRRDQQRNPGTST", "down_seq": "PSQPNSAGVQDTEMGPCRRH", "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": "Thr146", "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": "Thr146", "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" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "Other", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true, "automatic_literature_mining": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (HexNAc...) threonine;Other", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr146", "evidence": [ { "id": "P24592", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "id": "9572875", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9572875" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "snv": [ { "evidence": [ { "id": "rs765946180", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765946180" }, { "id": "rs765946180", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765946180" }, { "id": "rs765946180", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765946180#frequency_tab" }, { "id": "rs765946180", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765946180" }, { "id": "rs765946180", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765946180" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "12", "chr_pos": "53100814", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T146", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1212727893", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1212727893" }, { "id": "rs1212727893", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1212727893" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "12", "chr_pos": "53100813", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T146", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P24592-1.126.126", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P24592-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P24592-1.166.180", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "Identification of O-glycosylation sites and partial characterization of carbohydrate structure and disulfide linkages of human insulin-like growth factor binding protein 6.", "journal": "Biochemistry", "date": "1998", "authors": "Neumann GM, Marinaro JA, Bach LA", "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" }, { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875" } ] } ], "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": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9572875", "url": "https://glygen.org/publication/PubMed/9572875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P24592", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750463264", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750463264", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750463264", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750463264", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750463264", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750463264#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750463264", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750463264", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VNRRDQQRNPGTSTTPSQPN", "down_seq": "AGVQDTEMGPCRRHLDSVLQ", "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": "Ser152", "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": "S", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser152", "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" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "Other", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true, "automatic_literature_mining": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (HexNAc...) serine;Other", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser152", "evidence": [ { "id": "P24592", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P24592#ptm_processing" }, { "id": "9572875", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9572875" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "snv": [ { "evidence": [ { "id": "P24592", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592" }, { "id": "rs750463264", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750463264" }, { "id": "rs750463264", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750463264" }, { "id": "rs750463264", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750463264#frequency_tab" }, { "id": "rs750463264", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750463264" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "12", "chr_pos": "53100832", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S152", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P24592", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "12", "chr_pos": "53100832", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S152", "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": "P24592", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592" } ], "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": "12", "chr_pos": "53100832", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S152", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P24592-1.166.180", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.166.180", "start_pos": 166, "end_pos": 180, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "HLDSVLQQLQTEVYR", "start_aa": "H", "up_seq": "TPSQPNSAGVQDTEMGPCRR", "down_seq": "GAQTLYVPNCDHRGFYRKRQ", "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": "HLDSVLQQLQTEVYR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "His", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P24592-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P24592-1.176.176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 0, "direction": "upstream", "id": "P24592-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.181.193", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P24592-1.184.184", "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" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 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": "P24592-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.", "journal": "The EMBO journal", "date": "2013", "authors": "Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533" } ] }, { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "journal": "EMBO J", "date": "2013", "authors": "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs1367876993", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367876993", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1367876993", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1367876993", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QDTEMGPCRRHLDSVLQQLQ", "down_seq": "EVYRGAQTLYVPNCDHRGFY", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr176", "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": "rs1367876993", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367876993" }, { "id": "rs1367876993", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1367876993" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "12", "chr_pos": "53101087", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T176", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P24592-1.166.180", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P24592-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P24592-1.181.193", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.184.184", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.181.193", "start_pos": 181, "end_pos": 193, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "GAQTLYVPNCDHR", "start_aa": "G", "up_seq": "GPCRRHLDSVLQQLQTEVYR", "down_seq": "GFYRKRQCRSSQGQRRGPCW", "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": "GAQTLYVPNCDHR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Gly", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.166.180", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P24592-1.176.176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P24592-1.184.184", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P24592-1.204.204", "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": "P24592-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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" } ] }, { "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": "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": "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" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RRHLDSVLQQLQTEVYRGAQ", "down_seq": "LYVPNCDHRGFYRKRQCRSS", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr184", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P24592-1.166.180", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P24592-1.176.176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P24592-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.181.193", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P24592-1.204.204", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P24592-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Serine 204 phosphorylation and O-beta-GlcNAC interplay of IGFBP-6 as therapeutic indicator to regulate IGF-II functions in viral mediated hepatocellular carcinoma.", "journal": "Virology journal", "date": "2011", "authors": "Ahmad W, Shabbiri K, Ijaz B, Asad S, Nazar N, Nazar S, Fouzia K, Kausar H, Gull S, Sarwar MT, Shahid I, Hassan S", "evidence": [ { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "21548981", "url": "https://glygen.org/publication/PubMed/21548981" } ] } ], "crossref": [ { "id": "21548981", "url": "https://glygen.org/publication/PubMed/21548981", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P24592", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1937840023", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1937840023", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1937840023", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1937840023#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1937840023", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1937840023", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLYVPNCDHRGFYRKRQCRS", "down_seq": "QGQRRGPCWCVDRMGKSLPG", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "automatic_literature_mining", "site_category_dict": { "automatic_literature_mining": true }, "site_seq": "S", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser204", "evidence": [ { "id": "21548981", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21548981" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "RLIMS-G_1.0", "mining_tool_list": [ { "label": "RLIMS-G_1.0" } ] } ], "snv": [ { "evidence": [ { "id": "P24592", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592" }, { "id": "rs1937840023", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1937840023" }, { "id": "rs1937840023", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1937840023#frequency_tab" }, { "id": "rs1937840023", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1937840023" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "12", "chr_pos": "53102055", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S204", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P24592-1.181.193", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "downstream", "id": "P24592-1.184.184", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P24592-1.217.217", "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", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "P24592-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "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": "rs1053134", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1053134", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1053134", "url": "https://www.ensembl.org/id/rs1053134", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DRMGKSLPGSPDGNGSSSCP", "down_seq": "GSSG", "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": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr236", "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": "rs1053134", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1053134" }, { "id": "rs1053134", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1053134" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "12", "chr_pos": "53102150", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T236", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P24592-1.217.217", "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": "P24592-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371919194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371919194", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371919194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371919194", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371919194", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371919194#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371919194", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371919194", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LLGRGRCLPARAPAVAEENP", "down_seq": "ESKPQAGTARPQDVNRRDQQ", "snv": [ { "evidence": [ { "id": "rs371919194", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371919194" }, { "id": "rs371919194", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371919194" }, { "id": "rs371919194", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371919194#frequency_tab" }, { "id": "rs371919194", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371919194" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KES->NES).", "chr_id": "12", "chr_pos": "53100731", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K118", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P24592-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P24592-1.126.126", "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": "P24592-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P24592", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NRRDQQRNPGTSTTPSQPNS", "down_seq": "GVQDTEMGPCRRHLDSVLQQ", "snv": [ { "evidence": [ { "id": "P24592", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSA->NST).", "chr_id": "12", "chr_pos": "53100834", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A153", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P24592-1.109.134", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P24592-1.109.135", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P24592-1.119.134", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P24592-1.119.135", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P24592-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P24592-1.144.144", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P24592-1.145.145", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P24592-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P24592-1.152.152", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P24592-1.166.180", "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": "P24592-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P24592", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MGPCRRHLDSVLQQLQTEVY", "down_seq": "GAQTLYVPNCDHRGFYRKRQ", "snv": [ { "evidence": [ { "id": "P24592", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "53101098", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R180", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P24592-1.140.164", "categories": [ "glycosylation_flag" ] }, { "distance": 0, "direction": "downstream", "id": "P24592-1.166.180", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P24592-1.176.176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P24592-1.181.193", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P24592-1.184.184", "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": 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": "P24592-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "P24592-1", "length": 240, "uniprot_id": "IBP6_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 6", "refseq_ac": "NP_002169", "refseq_name": "insulin-like growth factor-binding protein 6 precursor", "gene_name": "IGFBP6", "gene_names_uniprotkb": "IGFBP6; IBP6", "gene_names_refseq": "IBP6; IGFBP6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P24592", "url": "https://www.uniprot.org/uniprotkb/P24592" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P24592", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RKRQCRSSQGQRRGPCWCVD", "down_seq": "MGKSLPGSPDGNGSSSCPTG", "snv": [ { "evidence": [ { "id": "P24592", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P24592" } ], "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": "53102093", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R217", "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": "109", "end_pos": "134" }, { "start_pos": "109", "end_pos": "135" }, { "start_pos": "119", "end_pos": "134" }, { "start_pos": "119", "end_pos": "135" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "140", "end_pos": "164" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "166", "end_pos": "180" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "181", "end_pos": "193" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "236", "end_pos": "236" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "236", "end_pos": "236" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P24592-1.204.204", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P24592-1.236.236", "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": "P42694-1.1260.1260", "start_pos": 1260, "end_pos": 1260, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs267605008", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605008", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs267605008", "url": "https://www.ensembl.org/id/rs267605008", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1598266106", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1598266106", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1598266106", "url": "https://www.ensembl.org/id/rs1598266106", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LQTHGRGSPIPYGLGHHPPV", "down_seq": "IGQPQNQHQEKDQHEQNRNG", "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": "Thr1260", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "P42694", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "P42694", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42694" } ] } ], "snv": [ { "evidence": [ { "id": "rs267605008", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605008" }, { "id": "rs267605008", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs267605008" } ], "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": "67120464", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1260", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1598266106", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1598266106" }, { "id": "rs1598266106", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1598266106" } ], "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": "67120465", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1260", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42694-1.1315.1315", "start_pos": 1315, "end_pos": 1315, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "rs2037219750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037219750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2037219750", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2037219750#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2037219750", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2037219750", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs771422651", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771422651", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771422651", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771422651", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771422651", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771422651", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RTPEKKPTEPKQVDLESNPQ", "down_seq": "RSPESRPSVVYPSTKFPRKD", "glycosylation": [ { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QVDLESNPQNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1315", "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": "rs2037219750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037219750" }, { "id": "rs2037219750", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2037219750#frequency_tab" }, { "id": "rs2037219750", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2037219750" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NRS->SRS).", "chr_id": "17", "chr_pos": "67109661", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1315", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs771422651", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771422651" }, { "id": "rs771422651", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771422651" }, { "id": "rs771422651", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771422651" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRS->YRS).", "chr_id": "17", "chr_pos": "67109662", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1315", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P42694-1.1311.1311", "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": "P42694-1.1882.1882", "start_pos": 1882, "end_pos": 1882, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLGQFPPLMPNKQIAESANS", "down_seq": "SPQSSAGGKPAMSYASALRA", "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": "Ser1882", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "P42694", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P42694-1.1883.1883", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42694-1.1901.1901", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42694-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "crossref": [ { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VKVEHNPDLSVTVSTKKSHQ", "down_seq": "WTFALTCKPARMLYRVALLY", "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": "Thr280", "evidence": [ { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" }, { "id": "P42694", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42694" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P42694-1.286.286", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42694-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "crossref": [ { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1443529087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443529087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443529087", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443529087", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PDLSVTVSTKKSHQTWTFAL", "down_seq": "CKPARMLYRVALLYDAHRPH", "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": "Thr286", "evidence": [ { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" }, { "id": "P42694", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42694" } ] } ], "snv": [ { "evidence": [ { "id": "rs1443529087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443529087" }, { "id": "rs1443529087", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443529087" } ], "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": "67189596", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T286", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P42694-1.280.280", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42694-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "rs749207696", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749207696", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749207696", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749207696", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749207696", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749207696", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LVTTAKRWDSSSKTIIDFEP", "down_seq": "ETTDLEKSLLIRYQIPLSAD", "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": "TIIDFEPNETTDLEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn419", "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": "rs749207696", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749207696" }, { "id": "rs749207696", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749207696" }, { "id": "rs749207696", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749207696" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NET->KET).", "chr_id": "17", "chr_pos": "67178832", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N419", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42694-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42694-1.421.421", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42694-1.563.563", "start_pos": 563, "end_pos": 563, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KLVQTQGTKEKVYEATIEEK", "down_seq": "KEYIFLRLSRECCEELNLRP", "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": "Thr563", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "P42694", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "P42694", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42694" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P42694-1.582.582", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42694-1.973.973", "start_pos": 973, "end_pos": 973, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "database": "O-GlcNAc Atlas", "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694" } ], "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": "P42694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "https://oglcnac.org/atlas/detail/P42694", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs779908316", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779908316", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779908316", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779908316#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779908316", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779908316", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VTPYADQVFRIRAELRKKRL", "down_seq": "DVNVERVLNVQGKQFRVLFL", "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": "Ser973", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "P42694", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42694" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "P42694", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42694" } ] } ], "snv": [ { "evidence": [ { "id": "rs779908316", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316" }, { "id": "rs779908316", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316" }, { "id": "rs779908316", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779908316#frequency_tab" }, { "id": "rs779908316", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779908316" } ], "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": "17", "chr_pos": "67137966", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S973", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779908316", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316" }, { "id": "rs779908316", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316" }, { "id": "rs779908316", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779908316#frequency_tab" }, { "id": "rs779908316", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779908316" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "17", "chr_pos": "67137966", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S973", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779908316", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316" }, { "id": "rs779908316", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779908316" }, { "id": "rs779908316", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779908316#frequency_tab" }, { "id": "rs779908316", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779908316" } ], "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": "17", "chr_pos": "67137966", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S973", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P42694-1.969.969", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42694-1.1107.1107", "start_pos": 1107, "end_pos": 1107, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The putative RNA helicase HELZ promotes cell proliferation, translation initiation and ribosomal protein S6 phosphorylation.", "journal": "PloS one", "date": "2011", "authors": "Hasgall PA, Hoogewijs D, Faza MB, Panse VG, Wenger RH, Camenisch G", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "reference": [ { "type": "PubMed", "id": "21765940", "url": "https://glygen.org/publication/PubMed/21765940" } ] }, { "title": "HELZ directly interacts with CCR4-NOT and causes decay of bound mRNAs.", "journal": "Life science alliance", "date": "2019-10", "authors": "Hanet Aoife, R\u00e4sch Felix, Weber Ramona, Ruscica Vincenzo, Fauser Maria, Raisch Tobias, Kuzuo\u011flu-\u00d6zt\u00fcrk Duygu, Chang Chung-Te, Bhandari Dipankar, Igreja C\u00e1tia, Wohlbold Lara", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "reference": [ { "type": "PubMed", "id": "31570513", "url": "https://glygen.org/publication/PubMed/31570513" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21765940", "url": "https://glygen.org/publication/PubMed/21765940", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31570513", "url": "https://glygen.org/publication/PubMed/31570513", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "AQLEALELKKTYVLNPLAPE", "down_seq": "IPRALRLQHSGSTNKQQQSP", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Loss of interaction with PABPC1.", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "21765940", "url": "https://glygen.org/publication/PubMed/21765940" } ] }, { "sequence_org": "F", "sequence_mut": "V", "comment": "Loss of interaction with PABPC1 but no effect on its ability to induce mRNA degradation and deadenylation-independent translational repression.", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "31570513", "url": "https://glygen.org/publication/PubMed/31570513" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42694-1.1095.1095", "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": "P42694-1.1018.1018", "start_pos": 1018, "end_pos": 1018, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TRHTCKHKQTPIKKKEQLLE", "down_seq": "STEDLDYGFLSNYKLLNTAI", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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 (DST->NST).", "chr_id": "17", "chr_pos": "67136100", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1018", "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1095.1095", "start_pos": 1095, "end_pos": 1095, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SSLHGITFEQIKAQLEALEL", "down_seq": "KTYVLNPLAPEFIPRALRLQ", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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 (KKT->NKT).", "chr_id": "17", "chr_pos": "67128753", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1095", "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P42694-1.1107.1107", "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": "P42694-1.1151.1151", "start_pos": 1151, "end_pos": 1151, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1221863604", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1221863604", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1221863604", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1221863604", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1221863604", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1221863604", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2037670550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037670550", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2037670550", "url": "https://www.ensembl.org/id/rs2037670550", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KSLHHTQNDHFQNDGIVQPN", "down_seq": "SVLIGNPIRAYTPPPPLGPH", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" }, { "id": "rs1221863604", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1221863604" }, { "id": "rs1221863604", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1221863604" }, { "id": "rs1221863604", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1221863604" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NHS).", "chr_id": "17", "chr_pos": "67123148", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1151", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NSS).", "chr_id": "17", "chr_pos": "67123149", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1151", "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": "rs2037670550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037670550" }, { "id": "rs2037670550", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2037670550" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NTS).", "chr_id": "17", "chr_pos": "67123149", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1151", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P42694-1.1163.1163", "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": 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": "P42694-1.1188.1188", "start_pos": 1188, "end_pos": 1188, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756070745", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756070745", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756070745", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756070745", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756070745", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756070745#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756070745", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756070745", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LGPHPNLGKSPSPVQRIDPH", "down_seq": "GTSILYVPAVYGGNVVMSVP", "snv": [ { "evidence": [ { "id": "rs756070745", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756070745" }, { "id": "rs756070745", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756070745" }, { "id": "rs756070745", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756070745#frequency_tab" }, { "id": "rs756070745", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756070745" } ], "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 (TGT->NGT).", "chr_id": "17", "chr_pos": "67123037", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1188", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P42694-1.1177.1177", "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": "P42694-1.1238.1238", "start_pos": 1238, "end_pos": 1238, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2143824366", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143824366", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2143824366", "url": "https://www.ensembl.org/id/rs2143824366", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GRFAVDPRIITHQAAMAYNM", "down_seq": "LLQTHGRGSPIPYGLGHHPP", "snv": [ { "evidence": [ { "id": "rs2143824366", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143824366" }, { "id": "rs2143824366", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2143824366" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NMN->NMS).", "chr_id": "17", "chr_pos": "67120530", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1238", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1282.1282", "start_pos": 1282, "end_pos": 1282, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1275609080", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275609080", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1275609080", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1275609080", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GQPQNQHQEKDQHEQNRNGK", "down_seq": "DTNNSGPEINKIRTPEKKPT", "snv": [ { "evidence": [ { "id": "rs1275609080", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275609080" }, { "id": "rs1275609080", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1275609080" } ], "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 (SDT->NDT).", "chr_id": "17", "chr_pos": "67114397", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1282", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P42694-1.1284.1284", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42694-1.1294.1294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1294.1294", "start_pos": 1294, "end_pos": 1294, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2037368024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037368024", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2037368024", "url": "https://www.ensembl.org/id/rs2037368024", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2037368024", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2037368024", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "HEQNRNGKSDTNNSGPEINK", "down_seq": "RTPEKKPTEPKQVDLESNPQ", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "I", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKI->NKS).", "chr_id": "17", "chr_pos": "67114361", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I1294", "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": "rs2037368024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2037368024" }, { "id": "rs2037368024", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2037368024" }, { "id": "rs2037368024", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2037368024" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKI->NKT).", "chr_id": "NC_000017.11", "chr_pos": "67114361", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "1e-06", "site_lbl": "I1294", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42694-1.1282.1282", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42694-1.1284.1284", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42694-1.1311.1311", "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": "P42694-1.1338.1338", "start_pos": 1338, "end_pos": 1338, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200263337", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200263337", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200263337", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200263337#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200263337", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200263337", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PESRPSVVYPSTKFPRKDNL", "down_seq": "PRHINLPLPAPHAQYAIPNR", "snv": [ { "evidence": [ { "id": "rs200263337", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200263337" }, { "id": "rs200263337", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200263337#frequency_tab" }, { "id": "rs200263337", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200263337" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLN->NLS).", "chr_id": "17", "chr_pos": "67109592", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1338", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P42694-1.1345.1345", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42694-1.1353.1353", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42694-1.1358.1358", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1345.1345", "start_pos": 1345, "end_pos": 1345, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs112975968", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs112975968", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs112975968", "url": "https://www.ensembl.org/id/rs112975968", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VYPSTKFPRKDNLNPRHINL", "down_seq": "LPAPHAQYAIPNRHFHPLPQ", "snv": [ { "evidence": [ { "id": "rs112975968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs112975968" }, { "id": "rs112975968", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs112975968" } ], "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": "17", "chr_pos": "67109572", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1345", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P42694-1.1338.1338", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42694-1.1353.1353", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42694-1.1358.1358", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1358.1358", "start_pos": 1358, "end_pos": 1358, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NPRHINLPLPAPHAQYAIPN", "down_seq": "HFHPLPQLPRPPFPIPQQHT", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "67109532", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1358", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42694-1.1338.1338", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42694-1.1345.1345", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42694-1.1353.1353", "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": "P42694-1.1388.1388", "start_pos": 1388, "end_pos": 1388, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1305034227", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1305034227", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1305034227", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1305034227#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1305034227", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1305034227", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "RPPFPIPQQHTLLNQQQNNL", "down_seq": "EQPNQIPPQPNQVVQQQSQL", "snv": [ { "evidence": [ { "id": "rs1305034227", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1305034227" }, { "id": "rs1305034227", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1305034227#frequency_tab" }, { "id": "rs1305034227", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1305034227" } ], "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": "17", "chr_pos": "67109443", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1388", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1431.1431", "start_pos": 1431, "end_pos": 1431, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750797081", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750797081", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750797081", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750797081", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750797081", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750797081", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "QPQQPPPQLSPAYQAGPNNA", "down_seq": "FNSAVAHRPQSPPAEAVIPE", "snv": [ { "evidence": [ { "id": "rs750797081", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750797081" }, { "id": "rs750797081", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750797081" }, { "id": "rs750797081", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750797081" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAF->NAS).", "chr_id": "17", "chr_pos": "67109313", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1431", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1487.1487", "start_pos": 1487, "end_pos": 1487, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2544516846", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2544516846", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AIAQPGPILPSHLNSFIDEN", "down_seq": "SGLPIGEALDRIHGSVALET", "snv": [ { "evidence": [ { "id": "rs2544516846", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2544516846" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NTS).", "chr_id": "17", "chr_pos": "67109146", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1487", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P42694-1.1498.1498", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1498.1498", "start_pos": 1498, "end_pos": 1498, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HLNSFIDENPSGLPIGEALD", "down_seq": "IHGSVALETLRQQQARFQQW", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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": "17", "chr_pos": "67108724", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1498", "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P42694-1.1487.1487", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1626.1626", "start_pos": 1626, "end_pos": 1626, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1349737021", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349737021", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1349737021", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349737021#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1349737021", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349737021", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QYRQVQSRSPPAVPSPPSST", "down_seq": "HSSHFSNFNDNSRDIEVASN", "snv": [ { "evidence": [ { "id": "rs1349737021", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349737021" }, { "id": "rs1349737021", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349737021#frequency_tab" }, { "id": "rs1349737021", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349737021" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DHS->NHS).", "chr_id": "17", "chr_pos": "67107534", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1626", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42694-1.1614.1614", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42694-1.1635.1635", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42694-1.1645.1645", "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": "P42694-1.1635.1635", "start_pos": 1635, "end_pos": 1635, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768954242", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768954242", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768954242", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768954242", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768954242", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768954242#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768954242", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768954242", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PPAVPSPPSSTDHSSHFSNF", "down_seq": "DNSRDIEVASNPAFPQRLPP", "snv": [ { "evidence": [ { "id": "rs768954242", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768954242" }, { "id": "rs768954242", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768954242" }, { "id": "rs768954242", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768954242#frequency_tab" }, { "id": "rs768954242", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768954242" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFN->NFS).", "chr_id": "17", "chr_pos": "67107506", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1635", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P42694-1.1626.1626", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42694-1.1645.1645", "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": "P42694-1.1762.1762", "start_pos": 1762, "end_pos": 1762, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779318703", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779318703", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779318703", "url": "https://www.ensembl.org/id/rs779318703", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LPSLEEYEPRGPGRPLYQRR", "down_seq": "SSSSVQPCSEEVSTPQDSLA", "snv": [ { "evidence": [ { "id": "rs779318703", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779318703" }, { "id": "rs779318703", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs779318703" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (ISS->NSS).", "chr_id": "17", "chr_pos": "67087038", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1762", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P42694-1.1763.1763", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42694-1.1766.1766", "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": "P42694-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LDEGSCNGWHFRPPPRGITS", "down_seq": "EEYTLCKRFLEQGICRYGAQ", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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": "17", "chr_pos": "67193990", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S178", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "P42694-1.1801.1801", "start_pos": 1801, "end_pos": 1801, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LAQCKELQDHSNQSSFNFSS", "down_seq": "ESWVNTTSSTPYQNIPCNGS", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "67086921", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1801", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P42694-1.1817.1817", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.1817.1817", "start_pos": 1817, "end_pos": 1817, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779446469", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779446469", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779446469", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779446469", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779446469", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779446469#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779446469", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779446469", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NFSSPESWVNTTSSTPYQNI", "down_seq": "CNGSSRTAQPRELIAPPKTV", "snv": [ { "evidence": [ { "id": "rs779446469", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779446469" }, { "id": "rs779446469", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779446469" }, { "id": "rs779446469", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779446469#frequency_tab" }, { "id": "rs779446469", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779446469" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIP->NIS).", "chr_id": "17", "chr_pos": "67086874", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1817", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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 (NIP->NIT).", "chr_id": "17", "chr_pos": "67086874", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1817", "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P42694-1.1801.1801", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P42694-1.1901.1901", "start_pos": 1901, "end_pos": 1901, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SSSPQSSAGGKPAMSYASAL", "down_seq": "APPKPRPPPEQAKKSSDPLS", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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 (5).", "chr_id": "17", "chr_pos": "67078380", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1901", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42694-1.1882.1882", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42694-1.1883.1883", "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": "P42694-1.247.247", "start_pos": 247, "end_pos": 247, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1457054304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457054304", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1457054304", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1457054304", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "ENKQLSGSYMETLIEKWMNS", "down_seq": "SPEKVLSECIEGVKVEHNPD", "snv": [ { "evidence": [ { "id": "rs1457054304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457054304" }, { "id": "rs1457054304", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1457054304" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSL->NSS).", "chr_id": "17", "chr_pos": "67190173", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L247", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P42694-1.248.248", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.316.316", "start_pos": 316, "end_pos": 316, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1159334465", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159334465", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1159334465", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159334465#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VALLYDAHRPHFSIIAISAG", "down_seq": "STTQVSQEVPENCQEWIGGK", "snv": [ { "evidence": [ { "id": "rs1159334465", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159334465" }, { "id": "rs1159334465", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159334465#frequency_tab" } ], "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": "17", "chr_pos": "67188535", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D316", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P42694-1.317.317", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.317.317", "start_pos": 317, "end_pos": 317, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767464522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767464522", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767464522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767464522", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767464522", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767464522", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALLYDAHRPHFSIIAISAGD", "down_seq": "TTQVSQEVPENCQEWIGGKM", "snv": [ { "evidence": [ { "id": "rs767464522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767464522" }, { "id": "rs767464522", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767464522" }, { "id": "rs767464522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767464522" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (STT->NTT).", "chr_id": "17", "chr_pos": "67188531", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S317", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P42694-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.407.407", "start_pos": 407, "end_pos": 407, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EDLEYLMHAKQQLVTTAKRW", "down_seq": "SSSKTIIDFEPNETTDLEKS", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "17", "chr_pos": "67178870", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D407", "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P42694-1.419.419", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42694-1.421.421", "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": "P42694-1.448.448", "start_pos": 448, "end_pos": 448, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1439226712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439226712", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1439226712", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1439226712#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1439226712", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1439226712", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLIRYQIPLSADQLFTQSVL", "down_seq": "KSLTKSNYQSRLHDLLYIEE", "snv": [ { "evidence": [ { "id": "rs1439226712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439226712" }, { "id": "rs1439226712", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1439226712#frequency_tab" }, { "id": "rs1439226712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1439226712" } ], "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": "17", "chr_pos": "67178747", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D448", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P42694-1.459.459", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.459.459", "start_pos": 459, "end_pos": 459, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DQLFTQSVLDKSLTKSNYQS", "down_seq": "LHDLLYIEEIAQYKEISKFN", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "67178713", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R459", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P42694-1.448.448", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.582.582", "start_pos": 582, "end_pos": 582, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KTKEYIFLRLSRECCEELNL", "down_seq": "PDCDTQVELQFQLNRLPLCE", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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 (4).", "chr_id": "17", "chr_pos": "67167483", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R582", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42694-1.563.563", "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": "P42694-1.621.621", "start_pos": 621, "end_pos": 621, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CEMHYALDRIKDNGVLFPDI", "down_seq": "MTPTIPWSPNRQWDEQLDPR", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SMT->NMT).", "chr_id": "17", "chr_pos": "67166511", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S621", "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": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.867.867", "start_pos": 867, "end_pos": 867, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RLYEHYPAEFPCRILLCENY", "down_seq": "SHEAIINYTSELFYEGKLMA", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "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": "17", "chr_pos": "67148590", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R867", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42694-1.969.969", "start_pos": 969, "end_pos": 969, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SIGVVTPYADQVFRIRAELR", "down_seq": "KRLSDVNVERVLNVQGKQFR", "snv": [ { "evidence": [ { "id": "P42694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42694" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "67137978", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K969", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P42694-1.973.973", "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": "P42694-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "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": "DAFRAVLCCMQLKGKLQPVS", "down_seq": "ILAKSLTGESLNGMVTKDLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr113" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "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": "P42694-1.1163.1163", "start_pos": 1163, "end_pos": 1163, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NDGIVQPNPSVLIGNPIRAY", "down_seq": "PPPPLGPHPNLGKSPSPVQR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "site_lbl": "Thr1163" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42694-1.1151.1151", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42694-1.1177.1177", "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": "P42694-1.1177.1177", "start_pos": 1177, "end_pos": 1177, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NPIRAYTPPPPLGPHPNLGK", "down_seq": "PSPVQRIDPHTGTSILYVPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ], "site_lbl": "Ser1177" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P42694-1.1163.1163", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42694-1.1188.1188", "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": "P42694-1.1284.1284", "start_pos": 1284, "end_pos": 1284, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "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": "PQNQHQEKDQHEQNRNGKSD", "down_seq": "NNSGPEINKIRTPEKKPTEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1284" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P42694-1.1282.1282", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42694-1.1294.1294", "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": "P42694-1.1311.1311", "start_pos": 1311, "end_pos": 1311, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "INKIRTPEKKPTEPKQVDLE", "down_seq": "NPQNRSPESRPSVVYPSTKF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser1311" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P42694-1.1294.1294", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42694-1.1315.1315", "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": "P42694-1.1353.1353", "start_pos": 1353, "end_pos": 1353, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A common phosphotyrosine signature for the Bcr-Abl kinase.", "journal": "Blood", "date": "2006", "authors": "Goss VL, Lee KA, Moritz A, Nardone J, Spek EJ, MacNeill J, Rush J, Comb MJ, Polakiewicz RD", "evidence": [ { "database": "iPTMnet", "id": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "16497976", "url": "https://glygen.org/publication/PubMed/16497976" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16497976", "url": "https://glygen.org/publication/PubMed/16497976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RKDNLNPRHINLPLPAPHAQ", "down_seq": "AIPNRHFHPLPQLPRPPFPI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "16497976", "url": "https://glygen.org/publication/PubMed/16497976" } ], "site_lbl": "Tyr1353" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P42694-1.1338.1338", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42694-1.1345.1345", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42694-1.1358.1358", "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": "P42694-1.1614.1614", "start_pos": 1614, "end_pos": 1614, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAEMPPPQSRLLQYRQVQSR", "down_seq": "PPAVPSPPSSTDHSSHFSNF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "site_lbl": "Ser1614" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P42694-1.1626.1626", "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": "P42694-1.1645.1645", "start_pos": 1645, "end_pos": 1645, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TDHSSHFSNFNDNSRDIEVA", "down_seq": "NPAFPQRLPPQIFNSPFSLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "site_lbl": "Ser1645" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42694-1.1626.1626", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42694-1.1635.1635", "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": "P42694-1.1738.1738", "start_pos": 1738, "end_pos": 1738, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "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": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNHQHAIGQEPFHPLSSRTV", "down_seq": "SSSLPSLEEYEPRGPGRPLY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "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": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "site_lbl": "Ser1738" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P42694-1.1739.1739", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42694-1.1741.1741", "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": "P42694-1.1739.1739", "start_pos": 1739, "end_pos": 1739, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "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": "NHQHAIGQEPFHPLSSRTVS", "down_seq": "SSLPSLEEYEPRGPGRPLYQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser1739" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P42694-1.1738.1738", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42694-1.1741.1741", "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": "P42694-1.1741.1741", "start_pos": 1741, "end_pos": 1741, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "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": "iPTMnet", "id": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "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": "QHAIGQEPFHPLSSRTVSSS", "down_seq": "LPSLEEYEPRGPGRPLYQRR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser1741" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P42694-1.1738.1738", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42694-1.1739.1739", "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": "P42694-1.1763.1763", "start_pos": 1763, "end_pos": 1763, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "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": "PSLEEYEPRGPGRPLYQRRI", "down_seq": "SSSVQPCSEEVSTPQDSLAQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser1763" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P42694-1.1762.1762", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42694-1.1766.1766", "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": "P42694-1.1766.1766", "start_pos": 1766, "end_pos": 1766, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEYEPRGPGRPLYQRRISSS", "down_seq": "VQPCSEEVSTPQDSLAQCKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "site_lbl": "Ser1766" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P42694-1.1762.1762", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42694-1.1763.1763", "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": "P42694-1.1883.1883", "start_pos": 1883, "end_pos": 1883, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "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": "LGQFPPLMPNKQIAESANSS", "down_seq": "PQSSAGGKPAMSYASALRAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser1883" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P42694-1.1882.1882", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42694-1.1901.1901", "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": "P42694-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NKQLSGSYMETLIEKWMNSL", "down_seq": "PEKVLSECIEGVKVEHNPDL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" } ], "site_lbl": "Ser248" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P42694-1.247.247", "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": "P42694-1.421.421", "start_pos": 421, "end_pos": 421, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "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": "TTAKRWDSSSKTIIDFEPNE", "down_seq": "TDLEKSLLIRYQIPLSADQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr421" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P42694-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42694-1.419.419", "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": "P42694-1.489.489", "start_pos": 489, "end_pos": 489, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "IEDB", "id": "193849", "url": "https://www.iedb.org/epitope/193849" }, { "database": "IEDB", "id": "219783", "url": "https://www.iedb.org/epitope/219783" }, { "database": "IEDB", "id": "491438", "url": "https://www.iedb.org/epitope/491438" }, { "database": "IEDB", "id": "541032", "url": "https://www.iedb.org/epitope/541032" }, { "database": "IEDB", "id": "541485", "url": "https://www.iedb.org/epitope/541485" }, { "database": "IEDB", "id": "543243", "url": "https://www.iedb.org/epitope/543243" }, { "database": "IEDB", "id": "604790", "url": "https://www.iedb.org/epitope/604790" }, { "database": "IEDB", "id": "614568", "url": "https://www.iedb.org/epitope/614568" }, { "database": "IEDB", "id": "634294", "url": "https://www.iedb.org/epitope/634294" }, { "database": "IEDB", "id": "654815", "url": "https://www.iedb.org/epitope/654815" }, { "database": "IEDB", "id": "1350585", "url": "https://www.iedb.org/epitope/1350585" }, { "database": "IEDB", "id": "1350646", "url": "https://www.iedb.org/epitope/1350646" }, { "database": "IEDB", "id": "1354311", "url": "https://www.iedb.org/epitope/1354311" }, { "database": "IEDB", "id": "1359880", "url": "https://www.iedb.org/epitope/1359880" }, { "database": "IEDB", "id": "1360806", "url": "https://www.iedb.org/epitope/1360806" }, { "database": "IEDB", "id": "1360878", "url": "https://www.iedb.org/epitope/1360878" }, { "database": "IEDB", "id": "1365693", "url": "https://www.iedb.org/epitope/1365693" }, { "database": "IEDB", "id": "1367813", "url": "https://www.iedb.org/epitope/1367813" }, { "database": "IEDB", "id": "1370868", "url": "https://www.iedb.org/epitope/1370868" }, { "database": "IEDB", "id": "1376554", "url": "https://www.iedb.org/epitope/1376554" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.iedb.org/epitope/P42694", "database": "IEDB", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IAQYKEISKFNLKVQLQILA", "down_seq": "FMLTGVSGGAKYAQNGQLFG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "P42694", "url": "https://www.iedb.org/epitope/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Ser489" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "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": "P42694-1.655.655", "start_pos": 655, "end_pos": 655, "uniprot_canonical_ac": "P42694-1", "length": 1942, "uniprot_id": "HELZ_HUMAN", "protein_name": "ATP-dependent RNA helicase with zinc finger domain", "refseq_ac": "XP_047293181", "refseq_name": "putative helicase with zinc finger domain isoform X4", "gene_name": "HELZ", "gene_names_uniprotkb": "HELZ; DRHC; KIAA0054", "gene_names_refseq": "DHRC; DRHC; HELZ; HUMORF5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42694", "url": "https://www.uniprot.org/uniprotkb/P42694" } ], "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": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "IEDB", "id": "193849", "url": "https://www.iedb.org/epitope/193849" }, { "database": "IEDB", "id": "219783", "url": "https://www.iedb.org/epitope/219783" }, { "database": "IEDB", "id": "491438", "url": "https://www.iedb.org/epitope/491438" }, { "database": "IEDB", "id": "541032", "url": "https://www.iedb.org/epitope/541032" }, { "database": "IEDB", "id": "541485", "url": "https://www.iedb.org/epitope/541485" }, { "database": "IEDB", "id": "543243", "url": "https://www.iedb.org/epitope/543243" }, { "database": "IEDB", "id": "604790", "url": "https://www.iedb.org/epitope/604790" }, { "database": "IEDB", "id": "614568", "url": "https://www.iedb.org/epitope/614568" }, { "database": "IEDB", "id": "634294", "url": "https://www.iedb.org/epitope/634294" }, { "database": "IEDB", "id": "654815", "url": "https://www.iedb.org/epitope/654815" }, { "database": "IEDB", "id": "1350585", "url": "https://www.iedb.org/epitope/1350585" }, { "database": "IEDB", "id": "1350646", "url": "https://www.iedb.org/epitope/1350646" }, { "database": "IEDB", "id": "1354311", "url": "https://www.iedb.org/epitope/1354311" }, { "database": "IEDB", "id": "1359880", "url": "https://www.iedb.org/epitope/1359880" }, { "database": "IEDB", "id": "1360806", "url": "https://www.iedb.org/epitope/1360806" }, { "database": "IEDB", "id": "1360878", "url": "https://www.iedb.org/epitope/1360878" }, { "database": "IEDB", "id": "1365693", "url": "https://www.iedb.org/epitope/1365693" }, { "database": "IEDB", "id": "1367813", "url": "https://www.iedb.org/epitope/1367813" }, { "database": "IEDB", "id": "1370868", "url": "https://www.iedb.org/epitope/1370868" }, { "database": "IEDB", "id": "1376554", "url": "https://www.iedb.org/epitope/1376554" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "P42694", "url": "https://www.iedb.org/epitope/P42694", "database": "IEDB", "categories": [ "Other" ] }, { "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DEQLDPRLNAKQKEAVLAIT", "down_seq": "PLAIQLPPVLIIGPYGTGKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "P42694", "url": "https://www.iedb.org/epitope/P42694" }, { "database": "iPTMnet", "id": "P42694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42694" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Thr655" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1882", "end_pos": "1882" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1107", "end_pos": "1107" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "1095", "end_pos": "1095" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1188", "end_pos": "1188" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "1431", "end_pos": "1431" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1498", "end_pos": "1498" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1635", "end_pos": "1635" }, { "start_pos": "1762", "end_pos": "1762" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1801", "end_pos": "1801" }, { "start_pos": "1817", "end_pos": "1817" }, { "start_pos": "1901", "end_pos": "1901" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "973", "end_pos": "973" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "1284", "end_pos": "1284" }, { "start_pos": "1311", "end_pos": "1311" }, { "start_pos": "1353", "end_pos": "1353" }, { "start_pos": "1614", "end_pos": "1614" }, { "start_pos": "1645", "end_pos": "1645" }, { "start_pos": "1738", "end_pos": "1738" }, { "start_pos": "1739", "end_pos": "1739" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1763", "end_pos": "1763" }, { "start_pos": "1766", "end_pos": "1766" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "655", "end_pos": "655" } ] } ], "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": "Q96FZ2-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "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": "rs1940415970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1940415970", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1940415970", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1940415970#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RRGQQRLPEWRDPDKYCPSY", "down_seq": "KSPQSNSPVLLSRLHFEKDA", "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": "YCPSYNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn43", "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": "rs1940415970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1940415970" }, { "id": "rs1940415970", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1940415970#frequency_tab" } ], "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": "3", "chr_pos": "129279859", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N43", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q96FZ2-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96FZ2-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "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": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification.", "journal": "Talanta", "date": "2017", "authors": "Shen B, Zhang W, Shi Z, Tian F, Deng Y, Sun C, Wang G, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811" } ] }, { "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": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" } ], "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": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" } ], "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": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "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": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96FZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811", "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": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "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": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q96FZ2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96FZ2" }, { "id": "28411811", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28411811" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q96FZ2-1.2.2", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q96FZ2-1.4.4", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96FZ2-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A non-proteolytic release mechanism for HMCES-DNA-protein crosslinks.", "journal": "The EMBO journal", "date": "2023-09-18", "authors": "Donsbach Maximilian, D\u00fcrauer Sophie, Gr\u00fcnert Florian, Nguyen Kha T, Nigam Richa, Yaneva Denitsa, Weickert Pedro, Bezalel-Buch Rachel, Semlow Daniel R, Stingele Julian", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "37519246", "url": "https://glygen.org/publication/PubMed/37519246" } ] }, { "title": "Self-reversal facilitates the resolution of HMCES DNA-protein crosslinks in cells.", "journal": "Cell reports", "date": "2023-11-28", "authors": "Rua-Fernandez Jorge, Lovejoy Courtney A, Mehta Kavi P M, Paulin Katherine A, Toudji Yasmine T, Giansanti Celeste, Eichman Brandt F, Cortez David", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "37950866", "url": "https://glygen.org/publication/PubMed/37950866" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37519246", "url": "https://glygen.org/publication/PubMed/37519246", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37950866", "url": "https://glygen.org/publication/PubMed/37950866", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SFKVPLGKGRRCVVLADGFY", "down_seq": "WQRCQGTNQRQPYFIYFPQI", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Abolished ability to mediate self-reversal of covalent cross-link with DNA in presence of double-stranded DNA.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "37519246", "url": "https://glygen.org/publication/PubMed/37519246" } ] }, { "sequence_org": "E", "sequence_mut": "Q", "comment": "Abolished ability to mediate self-reversal of covalent cross-link with DNA in presence of double-stranded DNA.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "37950866", "url": "https://glygen.org/publication/PubMed/37950866" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q96FZ2-1.137.137", "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": "Q96FZ2-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A non-proteolytic release mechanism for HMCES-DNA-protein crosslinks.", "journal": "The EMBO journal", "date": "2023-09-18", "authors": "Donsbach Maximilian, D\u00fcrauer Sophie, Gr\u00fcnert Florian, Nguyen Kha T, Nigam Richa, Yaneva Denitsa, Weickert Pedro, Bezalel-Buch Rachel, Semlow Daniel R, Stingele Julian", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "37519246", "url": "https://glygen.org/publication/PubMed/37519246" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37519246", "url": "https://glygen.org/publication/PubMed/37519246", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DVLYSYTIITVDSCKGLSDI", "down_seq": "HRMPAILDGEEAVSKWLDFG", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Decreased ability to mediate self-reversal of covalent cross-link with DNA in presence of double-stranded DNA.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "37519246", "url": "https://glygen.org/publication/PubMed/37519246" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q96FZ2-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96FZ2-1.212.212", "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": "Q96FZ2-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "HMCES Functions in the Alternative End-Joining Pathway of the DNA DSB Repair during Class Switch Recombination in B Cells.", "journal": "Molecular cell", "date": "2020", "authors": "Shukla V, Halabelian L, Balagere S, Samaniego-Castruita D, Feldman DE, Arrowsmith CH, Rao A, Aravind L", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "31806351", "url": "https://glygen.org/publication/PubMed/31806351" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31806351", "url": "https://glygen.org/publication/PubMed/31806351", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LYSYTIITVDSCKGLSDIHH", "down_seq": "MPAILDGEEAVSKWLDFGEV", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Abolished ability to bind DNA and abolished ability to promote class switch recombination (CSR) in B-cells.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "31806351", "url": "https://glygen.org/publication/PubMed/31806351" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q96FZ2-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96FZ2-1.210.210", "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": "Q96FZ2-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "HMCES Functions in the Alternative End-Joining Pathway of the DNA DSB Repair during Class Switch Recombination in B Cells.", "journal": "Molecular cell", "date": "2020", "authors": "Shukla V, Halabelian L, Balagere S, Samaniego-Castruita D, Feldman DE, Arrowsmith CH, Rao A, Aravind L", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "31806351", "url": "https://glygen.org/publication/PubMed/31806351" } ] }, { "title": "HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA.", "journal": "Cell", "date": "2019", "authors": "Mohni KN, Wessel SR, Zhao R, Wojciechowski AC, Luzwick JW, Layden H, Eichman BF, Thompson PS, Mehta KPM, Cortez D", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31806351", "url": "https://glygen.org/publication/PubMed/31806351", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "M", "down_seq": "GRTSCHLPRDVLTRACAYQD", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Cells are hypersensitive to ionizing radiations. Abolished ability to form a covalent cross-link with DNA. Does not affect single-stranded DNA (ssDNA)-binding. Does not affect ability to promote class switch recombination (CSR) in B-cells.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "31806351", "url": "https://glygen.org/publication/PubMed/31806351" }, { "database": "PubMed", "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q96FZ2-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96FZ2-1.4.4", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96FZ2-1.337.338", "start_pos": 337, "end_pos": 338, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA.", "journal": "Cell", "date": "2019", "authors": "Mohni KN, Wessel SR, Zhao R, Wojciechowski AC, Luzwick JW, Layden H, Eichman BF, Thompson PS, Mehta KPM, Cortez D", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "WL", "start_aa": "W", "up_seq": "QFLQKSPLPTKRGTAGLLEQ", "down_seq": "KREKEEEPVAKRPYSQ", "mutagenesis": [ { "sequence_org": "WL", "sequence_mut": "AA", "comment": "Abolished interaction with PCNA. Cells are hypersensitive to ionizing radiations.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q96FZ2-1.322.322", "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": "Q96FZ2-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.", "journal": "Nature structural & molecular biology", "date": "2019", "authors": "Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "31235913", "url": "https://glygen.org/publication/PubMed/31235913" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31235913", "url": "https://glygen.org/publication/PubMed/31235913", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MCG", "down_seq": "TSCHLPRDVLTRACAYQDRR", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Strongly reduced binding to single-stranded DNA.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "31235913", "url": "https://glygen.org/publication/PubMed/31235913" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q96FZ2-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96FZ2-1.2.2", "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": "Q96FZ2-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.", "journal": "Nature structural & molecular biology", "date": "2019", "authors": "Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "31235913", "url": "https://glygen.org/publication/PubMed/31235913" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31235913", "url": "https://glygen.org/publication/PubMed/31235913", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "KDADSSERIIAPMRWGLVPS", "down_seq": "FKESDPSKLQFNTTNCRSDT", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "E", "comment": "Strongly reduced binding to single-stranded DNA.", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "31235913", "url": "https://glygen.org/publication/PubMed/31235913" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q96FZ2-1.98.98", "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": "Q96FZ2-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA.", "journal": "Cell", "date": "2019", "authors": "Mohni KN, Wessel SR, Zhao R, Wojciechowski AC, Luzwick JW, Layden H, Eichman BF, Thompson PS, Mehta KPM, Cortez D", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96FZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96FZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1415931820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1415931820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1415931820", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1415931820#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1415931820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1415931820", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1415931820", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1415931820", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VPSWFKESDPSKLQFNTTNC", "down_seq": "SDTVMEKRSFKVPLGKGRRC", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Cells are hypersensitive to ionizing radiations. Abolished ability to form a covalent cross-link with DNA. Abolished binding to single-stranded DNA (ssDNA).", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "30554877", "url": "https://glygen.org/publication/PubMed/30554877" } ] } ], "snv": [ { "evidence": [ { "id": "Q96FZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96FZ2" }, { "id": "rs1415931820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1415931820" }, { "id": "rs1415931820", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1415931820#frequency_tab" }, { "id": "rs1415931820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1415931820" }, { "id": "rs1415931820", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1415931820" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NCR->NCC).", "chr_id": "3", "chr_pos": "129288962", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R98", "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": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q96FZ2-1.81.81", "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": "Q96FZ2-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96FZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96FZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs769226195", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769226195", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769226195", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769226195", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769226195", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769226195", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs769226195", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs769226195", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RCVVLADGFYEWQRCQGTNQ", "down_seq": "QPYFIYFPQIKTEKSGSIGA", "snv": [ { "evidence": [ { "id": "Q96FZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96FZ2" }, { "id": "rs769226195", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769226195" }, { "id": "rs769226195", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769226195" }, { "id": "rs769226195", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769226195" }, { "id": "rs769226195", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs769226195" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NQR->NQS).", "chr_id": "3", "chr_pos": "129290762", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R137", "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": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q96FZ2-1.127.127", "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": "Q96FZ2-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1229816967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229816967", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1229816967", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1229816967#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SGSIGAADSPENWEKVWDNW", "down_seq": "LLTMAGIFDCWEPPEGGDVL", "snv": [ { "evidence": [ { "id": "rs1229816967", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229816967" }, { "id": "rs1229816967", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1229816967#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NWR->NWS).", "chr_id": "3", "chr_pos": "129298416", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q96FZ2-1.160.160", "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": "Q96FZ2-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1010024752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1010024752", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1010024752", "url": "https://www.ensembl.org/id/rs1010024752", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "AGIFDCWEPPEGGDVLYSYT", "down_seq": "ITVDSCKGLSDIHHRMPAIL", "snv": [ { "evidence": [ { "id": "rs1010024752", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1010024752" }, { "id": "rs1010024752", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1010024752" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IIT->NIT).", "chr_id": "3", "chr_pos": "129298490", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I197", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q96FZ2-1.210.210", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q96FZ2-1.212.212", "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": "Q96FZ2-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372612340", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372612340", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372612340", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372612340", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372612340", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372612340#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372612340", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372612340", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TENITFHAVSSVVNNSRNNT", "down_seq": "ECLAPVDLVVKKELRASGSS", "snv": [ { "evidence": [ { "id": "rs372612340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372612340" }, { "id": "rs372612340", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372612340" }, { "id": "rs372612340", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372612340#frequency_tab" }, { "id": "rs372612340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372612340" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTP->NTS).", "chr_id": "3", "chr_pos": "129302104", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P264", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96FZ2-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1173998980", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173998980", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1173998980", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173998980", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GQQRLPEWRDPDKYCPSYNK", "down_seq": "PQSNSPVLLSRLHFEKDADS", "snv": [ { "evidence": [ { "id": "rs1173998980", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173998980" }, { "id": "rs1173998980", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173998980" } ], "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 (NKS->NKN).", "chr_id": "3", "chr_pos": "129279866", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S45", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q96FZ2-1.43.43", "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": "Q96FZ2-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "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": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "iPTMnet", "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2", "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": "YFIYFPQIKTEKSGSIGAAD", "down_seq": "PENWEKVWDNWRLLTMAGIF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser160" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q96FZ2-1.172.172", "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": "Q96FZ2-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "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": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "iPTMnet", "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKELRASGSSQRMLQWLATK", "down_seq": "PKKEDSKTPQKEESDVPQWS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" } ], "site_lbl": "Ser295" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "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": "Q96FZ2-1.322.322", "start_pos": 322, "end_pos": 322, "uniprot_canonical_ac": "Q96FZ2-1", "length": 354, "uniprot_id": "HMCES_HUMAN", "protein_name": "Abasic site processing protein HMCES", "refseq_ac": "NP_001006109", "refseq_name": "abasic site processing protein HMCES isoform a", "gene_name": "HMCES", "gene_names_uniprotkb": "HMCES; C3orf37; DC12; SRAPD1", "gene_names_refseq": "C3orf37; DC12; HMCES; SRAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" } ], "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": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "iPTMnet", "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" } ], "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": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2", "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": "KTPQKEESDVPQWSSQFLQK", "down_seq": "PLPTKRGTAGLLEQWLKREK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96FZ2", "url": "https://www.uniprot.org/uniprotkb/Q96FZ2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q96FZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96FZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser322" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "43", "end_pos": "43" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "337", "end_pos": "338" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "snv", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q96FZ2-1.337.338", "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": "P14317-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "database": "O-GlcNAc Atlas", "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "database": "O-GlcNAc Atlas", "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "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": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "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": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PAPLPKKISSEAWPPVGTPP", "down_seq": "SESEPVRTSREHPVPLLPIR", "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": "Ser311", "evidence": [ { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "P14317", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "P14317", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P14317" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P14317-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P14317-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P14317-1.312.312", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P14317-1.314.314", "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": "P14317-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "database": "O-GlcNAc Atlas", "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "database": "O-GlcNAc Atlas", "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites.", "journal": "Molecular & cellular proteomics : MCP", "date": "2021", "authors": "Maynard JC, Chalkley RJ", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "crossref": [ { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs779203250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779203250", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779203250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779203250", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779203250", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779203250#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779203250", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779203250", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APLPKKISSEAWPPVGTPPS", "down_seq": "ESEPVRTSREHPVPLLPIRQ", "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": "Ser312", "evidence": [ { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "P14317", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "P14317", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P14317" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" } ] }, { "glytoucan_ac": "G70994MS", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser312", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "GLY_000142", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000142" } ] } ], "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "3", "chr_pos": "121633140", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S312", "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": "rs779203250", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779203250" }, { "id": "rs779203250", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779203250" }, { "id": "rs779203250", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779203250#frequency_tab" }, { "id": "rs779203250", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779203250" } ], "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": "3", "chr_pos": "121633141", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S312", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P14317-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P14317-1.311.311", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P14317-1.314.314", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P14317-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "database": "O-GlcNAc Atlas", "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "database": "O-GlcNAc Atlas", "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://oglcnac.org/atlas/detail/P14317", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1203104140", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203104140", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1203104140", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203104140", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPKKISSEAWPPVGTPPSSE", "down_seq": "EPVRTSREHPVPLLPIRQTL", "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": "Ser314", "evidence": [ { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "P14317", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P14317" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "P14317", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P14317" } ] } ], "snv": [ { "evidence": [ { "id": "rs1203104140", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203104140" }, { "id": "rs1203104140", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203104140" } ], "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": "3", "chr_pos": "121633134", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S314", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P14317-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P14317-1.311.311", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P14317-1.312.312", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P14317-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1394521622", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394521622", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1394521622", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394521622", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1394521622", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1394521622", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SQTDAAKGFGGKYGVERDRA", "down_seq": "KSAVGFDYKGEVEKHTSQKD", "snv": [ { "evidence": [ { "id": "rs1394521622", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394521622" }, { "id": "rs1394521622", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394521622" }, { "id": "rs1394521622", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1394521622" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DKS->NKS).", "chr_id": "3", "chr_pos": "121644823", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D132", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P14317-1.140.140", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P14317-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P14317-1.148.148", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1224882179", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1224882179", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1224882179", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1224882179#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "ERDRADKSAVGFDYKGEVEK", "down_seq": "TSQKDYSRGFGGRYGVEKDK", "snv": [ { "evidence": [ { "id": "rs1224882179", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1224882179" }, { "id": "rs1224882179", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1224882179#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HTS->NTS).", "chr_id": "3", "chr_pos": "121642942", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H147", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P14317-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P14317-1.140.140", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P14317-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P14317-1.162.162", "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": "P14317-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GEVEKHTSQKDYSRGFGGRY", "down_seq": "VEKDKWDKAALGYDYKGETE", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "121637227", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G162", "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: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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P14317-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P14317-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P14317-1.179.179", "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": "P14317-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GRYGVEKDKWDKAALGYDYK", "down_seq": "ETEKHESQRDYAKGFGGQYG", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "121637176", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G179", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P14317-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P14317-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P14317-1.198.198", "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": "P14317-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KDKWDKAALGYDYKGETEKH", "down_seq": "SQRDYAKGFGGQYGIQKDRV", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "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": "121637158", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E185", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P14317-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P14317-1.198.198", "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": "P14317-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759812697", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759812697", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759812697", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759812697", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759812697", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759812697", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SQRDYAKGFGGQYGIQKDRV", "down_seq": "KSAVGFNEMEAPTTAYKKTT", "snv": [ { "evidence": [ { "id": "rs759812697", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759812697" }, { "id": "rs759812697", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759812697" }, { "id": "rs759812697", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759812697" } ], "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": "3", "chr_pos": "121636439", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D206", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P14317-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P14317-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P14317-1.225.225", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VDKSAVGFNEMEAPTTAYKK", "down_seq": "TPIEAASSGTRGLKAKFESM", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "121635752", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T225", "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: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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P14317-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P14317-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P14317-1.233.233", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.233.233", "start_pos": 233, "end_pos": 233, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1268860206", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1268860206", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1268860206", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1268860206#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1268860206", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1268860206", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NEMEAPTTAYKKTTPIEAAS", "down_seq": "GTRGLKAKFESMAEEKRKRE", "snv": [ { "evidence": [ { "id": "rs1268860206", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1268860206" }, { "id": "rs1268860206", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1268860206#frequency_tab" }, { "id": "rs1268860206", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1268860206" } ], "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": "3", "chr_pos": "121634412", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S233", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P14317-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P14317-1.225.225", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VTKRSPEAPQPVIAMEEPAV", "down_seq": "APLPKKISSEAWPPVGTPPS", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "121634238", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P291", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P14317-1.275.275", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P14317-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P14317-1.311.311", "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": "P14317-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Role of tyrosine phosphorylation of HS1 in B cell antigen receptor-mediated apoptosis.", "journal": "The Journal of experimental medicine", "date": "1997", "authors": "Yamanashi Y, Fukuda T, Nishizumi H, Inazu T, Higashi K, Kitamura D, Ishida T, Yamamura H, Watanabe T, Yamamoto T", "evidence": [ { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" } ] }, { "title": "HS1 functions as an essential actin-regulatory adaptor protein at the immune synapse.", "journal": "Immunity", "date": "2006", "authors": "Gomez TS, McCarney SD, Carrizosa E, Labno CM, Comiskey EO, Nolz JC, Zhu P, Freedman BD, Clark MR, Rawlings DJ, Billadeau DD, Burkhardt JK", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "16782030", "url": "https://glygen.org/publication/PubMed/16782030" } ] }, { "title": "Wnt5a induces ROR1 to complex with HS1 to enhance migration of chronic lymphocytic leukemia cells.", "journal": "Leukemia", "date": "2017", "authors": "Hasan MK, Yu J, Chen L, Cui B, Widhopf Ii GF, Rassenti L, Shen Z, Briggs SP, Kipps TJ", "evidence": [ { "database": "RefSeq", "id": "NP_005326", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_005326" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "28465529", "url": "https://glygen.org/publication/PubMed/28465529" } ] }, { "title": "Hematopoietic lineage cell-specific protein 1 (HS1), a hidden player in migration, invasion, and tumor formation, is over-expressed in ovarian carcinoma cells.", "journal": "Oncotarget", "date": "2018", "authors": "Koya Y, Liu W, Yamakita Y, Senga T, Shibata K, Yamashita M, Nawa A, Kikkawa F, Kajiyama H", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969" } ] } ], "crossref": [ { "id": "rs745714416", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745714416", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745714416", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745714416", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745714416", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745714416#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745714416", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745714416", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16782030", "url": "https://glygen.org/publication/PubMed/16782030", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28465529", "url": "https://glygen.org/publication/PubMed/28465529", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PVYEAEPEPEPEPEPEPEND", "down_seq": "EDVEEMDRHEQEDEPEGDYE", "snv": [ { "evidence": [ { "id": "rs745714416", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745714416" }, { "id": "rs745714416", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745714416" }, { "id": "rs745714416", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745714416#frequency_tab" }, { "id": "rs745714416", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745714416" } ], "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 (NDY->NDC).", "chr_id": "3", "chr_pos": "121632439", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y378", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P07948-1", "kinase_gene_name": "LYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" } ], "site_lbl": "Tyr378" }, { "kinase_uniprot_canonical_ac": "P43405-1", "kinase_gene_name": "SYK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" }, { "database": "PubMed", "id": "16782030", "url": "https://glygen.org/publication/PubMed/16782030" } ], "site_lbl": "Tyr378" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by SYK and FES", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "28465529", "url": "https://glygen.org/publication/PubMed/28465529" }, { "database": "PubMed", "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969" }, { "database": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" } ], "site_lbl": "Tyr378" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P14317-1.397.397", "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": 3 } ], "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P14317-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QGDDWDTDPDFVNDISEKEQ", "down_seq": "WGAKTIEGSGRTEHINIHQL", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "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": "3", "chr_pos": "121657328", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R37", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P14317-1.23.23", "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": "P14317-1.436.436", "start_pos": 436, "end_pos": 436, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SGCPAGAGAGAVALGISAVA", "down_seq": "YDYQGEGSDELSFDPDDVIT", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "14", "frequency": "0.3", "sequence_org": "V", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: patient count (14/4799).", "chr_id": "3", "chr_pos": "121632119", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "V436", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "P14317-1.453.453", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AVAVYDYQGEGSDELSFDPD", "down_seq": "VITDIEMVDEGWWRGRCHGH", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "121631950", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D453", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P14317-1.436.436", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P14317-1.472.472", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.472.472", "start_pos": 472, "end_pos": 472, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DDVITDIEMVDEGWWRGRCH", "down_seq": "HFGLFPANYVKLLE", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "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": "3", "chr_pos": "121631892", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G472", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P14317-1.453.453", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AKTIEGSGRTEHINIHQLRN", "down_seq": "VSEEHDVLRKKEMESGPKAS", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1557", "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": "3", "chr_pos": "121647427", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K60", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P14317-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MESGPKASHGYGGRFGVERD", "down_seq": "MDKSAVGHEYVAEVEKHSSQ", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "121647329", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R93", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P14317-1.103.103", "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": "P14317-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MWKSVVGH", "down_seq": "VSVSVETQGDDWDTDPDFVN", "snv": [ { "evidence": [ { "id": "P14317", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P14317" } ], "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 (DVS->NVS).", "chr_id": "3", "chr_pos": "121658323", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D9", "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": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P14317-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P14317-1.23.23", "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": "P14317-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2005", "authors": "Ficarro SB, Salomon AR, Brill LM, Mason DE, Stettler-Gill M, Brock A, Peters EC", "evidence": [ { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "15570572", "url": "https://glygen.org/publication/PubMed/15570572" } ] } ], "crossref": [ { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15570572", "url": "https://glygen.org/publication/PubMed/15570572", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YGGRFGVERDRMDKSAVGHE", "down_seq": "VAEVEKHSSQTDAAKGFGGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "15570572", "url": "https://glygen.org/publication/PubMed/15570572" } ], "site_lbl": "Tyr103" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P14317-1.93.93", "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": "P14317-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "FGGKYGVERDRADKSAVGFD", "down_seq": "KGEVEKHTSQKDYSRGFGGR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "site_lbl": "Tyr140" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P14317-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P14317-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P14317-1.148.148", "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": "P14317-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "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": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "P14317", "url": "https://www.iedb.org/epitope/P14317", "database": "IEDB", "categories": [ "Other" ] }, { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "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": "RDRADKSAVGFDYKGEVEKH", "down_seq": "SQKDYSRGFGGRYGVEKDKW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "P14317", "url": "https://www.iedb.org/epitope/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr148" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P14317-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P14317-1.140.140", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P14317-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P14317-1.162.162", "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": "P14317-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Ser/Thr phosphorylation of hematopoietic specific protein 1 (HS1): implication of protein kinase CK2.", "journal": "European journal of biochemistry", "date": "2000", "authors": "Ruzzene M, Brunati AM, Sarno S, Marin O, Donella-Deana A, Pinna LA", "evidence": [ { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "10806407", "url": "https://glygen.org/publication/PubMed/10806407" } ] } ], "crossref": [ { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10806407", "url": "https://glygen.org/publication/PubMed/10806407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MWKSVVGHDVSVSVE", "down_seq": "QGDDWDTDPDFVNDISEKEQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P68400-1", "kinase_gene_name": "CSNK2A1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "10806407", "url": "https://glygen.org/publication/PubMed/10806407" } ], "site_lbl": "Thr16" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P14317-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P14317-1.23.23", "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": "P14317-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2003", "authors": "Salomon AR, Ficarro SB, Brill LM, Brinker A, Phung QT, Ericson C, Sauer K, Brock A, Horn DM, Schultz PG, Peters EC", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "12522270", "url": "https://glygen.org/publication/PubMed/12522270" } ] }, { "title": "Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry.", "journal": "Analytical chemistry", "date": "2004", "authors": "Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M, Peters EC", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] } ], "crossref": [ { "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12522270", "url": "https://glygen.org/publication/PubMed/12522270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KGETEKHESQRDYAKGFGGQ", "down_seq": "GIQKDRVDKSAVGFNEMEAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "PubMed", "id": "12522270", "url": "https://glygen.org/publication/PubMed/12522270" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "site_lbl": "Tyr198" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P14317-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P14317-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P14317-1.206.206", "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": "P14317-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular features underlying the sequential phosphorylation of HS1 protein and its association with c-Fgr protein-tyrosine kinase.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Brunati AM, Donella-Deana A, James P, Quadroni M, Contri A, Marin O, Pinna LA", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "10066823", "url": "https://glygen.org/publication/PubMed/10066823" } ] }, { "title": "Hematopoietic lineage cell-specific protein 1 (HS1), a hidden player in migration, invasion, and tumor formation, is over-expressed in ovarian carcinoma cells.", "journal": "Oncotarget", "date": "2018", "authors": "Koya Y, Liu W, Yamakita Y, Senga T, Shibata K, Yamashita M, Nawa A, Kikkawa F, Kajiyama H", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969" } ] }, { "title": "SH2 domains mediate the sequential phosphorylation of HS1 protein by p72syk and Src-related protein tyrosine kinases.", "journal": "Biochemistry", "date": "1996", "authors": "Ruzzene M, Brunati AM, Marin O, Donella-Deana A, Pinna LA", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "8611520", "url": "https://glygen.org/publication/PubMed/8611520" } ] } ], "crossref": [ { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10066823", "url": "https://glygen.org/publication/PubMed/10066823", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8611520", "url": "https://glygen.org/publication/PubMed/8611520", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KDRVDKSAVGFNEMEAPTTA", "down_seq": "KKTTPIEAASSGTRGLKAKF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P07948-1", "kinase_gene_name": "LYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "10066823", "url": "https://glygen.org/publication/PubMed/10066823" } ], "site_lbl": "Tyr222" }, { "kinase_uniprot_canonical_ac": "P09769-1", "kinase_gene_name": "FGR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "10066823", "url": "https://glygen.org/publication/PubMed/10066823" } ], "site_lbl": "Tyr222" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by FGR", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "10066823", "url": "https://glygen.org/publication/PubMed/10066823" }, { "database": "PubMed", "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969" }, { "database": "PubMed", "id": "8611520", "url": "https://glygen.org/publication/PubMed/8611520" } ], "site_lbl": "Tyr222" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P14317-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P14317-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P14317-1.233.233", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P14317-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Ser/Thr phosphorylation of hematopoietic specific protein 1 (HS1): implication of protein kinase CK2.", "journal": "European journal of biochemistry", "date": "2000", "authors": "Ruzzene M, Brunati AM, Sarno S, Marin O, Donella-Deana A, Pinna LA", "evidence": [ { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "10806407", "url": "https://glygen.org/publication/PubMed/10806407" } ] } ], "crossref": [ { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10806407", "url": "https://glygen.org/publication/PubMed/10806407", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSVVGHDVSVSVETQGDDWD", "down_seq": "DPDFVNDISEKEQRWGAKTI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P68400-1", "kinase_gene_name": "CSNK2A1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "10806407", "url": "https://glygen.org/publication/PubMed/10806407" } ], "site_lbl": "Thr23" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P14317-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P14317-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P14317-1.37.37", "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": "P14317-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "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": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry.", "journal": "Nature methods", "date": "2005", "authors": "Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R", "evidence": [ { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "16094384", "url": "https://glygen.org/publication/PubMed/16094384" } ] } ], "crossref": [ { "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16094384", "url": "https://glygen.org/publication/PubMed/16094384", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEKAQQVARRQQERKAVTKR", "down_seq": "PEAPQPVIAMEEPAVPAPLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "16094384", "url": "https://glygen.org/publication/PubMed/16094384" } ], "site_lbl": "Ser275" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P14317-1.291.291", "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": "P14317-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "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": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "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": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] } ], "crossref": [ { "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317", "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": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PAVPAPLPKKISSEAWPPVG", "down_seq": "PPSSESEPVRTSREHPVPLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "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": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "site_lbl": "Thr308" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P14317-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P14317-1.311.311", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P14317-1.312.312", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P14317-1.314.314", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P14317-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "P14317-1", "length": 486, "uniprot_id": "HCLS1_HUMAN", "protein_name": "Hematopoietic lineage cell-specific protein", "refseq_ac": "NP_005326", "refseq_name": "hematopoietic lineage cell-specific protein isoform 1", "gene_name": "HCLS1", "gene_names_uniprotkb": "HCLS1; HS1", "gene_names_refseq": "CTTNL; HCLS1; HS1; lckBP1; p75", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Role of tyrosine phosphorylation of HS1 in B cell antigen receptor-mediated apoptosis.", "journal": "The Journal of experimental medicine", "date": "1997", "authors": "Yamanashi Y, Fukuda T, Nishizumi H, Inazu T, Higashi K, Kitamura D, Ishida T, Yamamura H, Watanabe T, Yamamoto T", "evidence": [ { "database": "iPTMnet", "id": "P14317-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317-1" } ], "reference": [ { "type": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" } ] }, { "title": "HS1 functions as an essential actin-regulatory adaptor protein at the immune synapse.", "journal": "Immunity", "date": "2006", "authors": "Gomez TS, McCarney SD, Carrizosa E, Labno CM, Comiskey EO, Nolz JC, Zhu P, Freedman BD, Clark MR, Rawlings DJ, Billadeau DD, Burkhardt JK", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "16782030", "url": "https://glygen.org/publication/PubMed/16782030" } ] }, { "title": "Thrombin-induced tyrosine phosphorylation of HS1 in human platelets is sequentially catalyzed by Syk and Lyn tyrosine kinases and associated with the cellular migration of the protein.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Brunati AM, Deana R, Folda A, Massimino ML, Marin O, Ledro S, Pinna LA, Donella-Deana A", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "15795233", "url": "https://glygen.org/publication/PubMed/15795233" } ] }, { "title": "Specific stimulation of c-Fgr kinase by tyrosine-phosphorylated (poly)peptides--possible implication in the sequential mode of protein phosphorylation.", "journal": "European journal of biochemistry", "date": "1997", "authors": "Ruzzene M, Brunati AM, Donella-Deana A, Marin O, Pinna LA", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "9183008", "url": "https://glygen.org/publication/PubMed/9183008" } ] }, { "title": "Targeting the LYN/HS1 signaling axis in chronic lymphocytic leukemia.", "journal": "Blood", "date": "2013", "authors": "ten Hacken E, Scielzo C, Bertilaccio MT, Scarfo L, Apollonio B, Barbaglio F, Stamatopoulos K, Ponzoni M, Ghia P, Caligaris-Cappio F", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "23325840", "url": "https://glygen.org/publication/PubMed/23325840" } ] }, { "title": "Establishment and Characterization of PCL12, a Novel CD5+ Chronic Lymphocytic Leukaemia Cell Line.", "journal": "PloS one", "date": "2015", "authors": "Agathangelidis A, Scarfo L, Barbaglio F, Apollonio B, Bertilaccio MT, Ranghetti P, Ponzoni M, Leone G, De Pascali V, Pecciarini L, Ghia P, Caligaris-Cappio F, Scielzo C", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "26110819", "url": "https://glygen.org/publication/PubMed/26110819" } ] }, { "title": "Hematopoietic lineage cell-specific protein 1 (HS1), a hidden player in migration, invasion, and tumor formation, is over-expressed in ovarian carcinoma cells.", "journal": "Oncotarget", "date": "2018", "authors": "Koya Y, Liu W, Yamakita Y, Senga T, Shibata K, Yamashita M, Nawa A, Kikkawa F, Kajiyama H", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" } ], "reference": [ { "type": "PubMed", "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969" } ] } ], "crossref": [ { "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16782030", "url": "https://glygen.org/publication/PubMed/16782030", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P14317", "url": "https://www.ebi.ac.uk/intact/interactors/id:P14317*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "15795233", "url": "https://glygen.org/publication/PubMed/15795233", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9183008", "url": "https://glygen.org/publication/PubMed/9183008", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23325840", "url": "https://glygen.org/publication/PubMed/23325840", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26110819", "url": "https://glygen.org/publication/PubMed/26110819", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DYEDVEEMDRHEQEDEPEGD", "down_seq": "EEVLEPEDSSFSSALAGSSG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P07948-1", "kinase_gene_name": "LYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" } ], "site_lbl": "Tyr397" }, { "kinase_uniprot_canonical_ac": "P43405-1", "kinase_gene_name": "SYK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" }, { "database": "PubMed", "id": "16782030", "url": "https://glygen.org/publication/PubMed/16782030" } ], "site_lbl": "Tyr397" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by SYK and FES", "evidence": [ { "database": "UniProtKB", "id": "P14317", "url": "https://www.uniprot.org/uniprotkb/P14317" }, { "database": "IntAct", "id": "P14317", "url": "https://www.ebi.ac.uk/intact/interactors/id:P14317*" }, { "database": "iPTMnet", "id": "P14317", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P14317" }, { "database": "PubMed", "id": "15795233", "url": "https://glygen.org/publication/PubMed/15795233" }, { "database": "PubMed", "id": "9183008", "url": "https://glygen.org/publication/PubMed/9183008" }, { "database": "PubMed", "id": "23325840", "url": "https://glygen.org/publication/PubMed/23325840" }, { "database": "PubMed", "id": "26110819", "url": "https://glygen.org/publication/PubMed/26110819" }, { "database": "PubMed", "id": "30220969", "url": "https://glygen.org/publication/PubMed/30220969" }, { "database": "PubMed", "id": "9104825", "url": "https://glygen.org/publication/PubMed/9104825" } ], "site_lbl": "Tyr397" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" } ] }, { "type": "snv", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "397", "end_pos": "397" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P14317-1.378.378", "categories": [ "snv_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 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": "Q9H098-1.131.131", "start_pos": 131, "end_pos": 131, "uniprot_canonical_ac": "Q9H098-1", "length": 131, "uniprot_id": "F107B_HUMAN", "protein_name": "Protein FAM107B", "refseq_ac": "NP_001269624", "refseq_name": "protein FAM107B isoform a", "gene_name": "FAM107B", "gene_names_uniprotkb": "FAM107B; C10orf45", "gene_names_refseq": "C10orf45; FAM107B; HITS", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H098", "url": "https://www.uniprot.org/uniprotkb/Q9H098" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H098", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H098", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FVKVKGNLRRTGQEVAQAQE", "down_seq": "", "snv": [ { "evidence": [ { "id": "Q9H098", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H098" } ], "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": "10", "chr_pos": "14774272", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S131", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "131", "end_pos": "131" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P4H8-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q6P4H8-1", "length": 233, "uniprot_id": "ACKMT_HUMAN", "protein_name": "ATP synthase subunit C lysine N-methyltransferase", "refseq_ac": "NP_001245317", "refseq_name": "ATP synthase subunit C lysine N-methyltransferase isoform 2", "gene_name": "ATPSCKMT", "gene_names_uniprotkb": "ATPSCKMT; FAM173B", "gene_names_refseq": "ATPSCKMT; FAM173B; JS-2; hFAM173B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" } ], "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": "Q6P4H8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750764838", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750764838", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750764838", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750764838", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750764838", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750764838#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750764838", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750764838", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750764838", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750764838", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LTGLVGGTLVAVYAVATPFV", "down_seq": "PALRKVCLPFVPATTKQIEN", "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": "Thr60", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "Q6P4H8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8" }, { "id": "rs750764838", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750764838" }, { "id": "rs750764838", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750764838" }, { "id": "rs750764838", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750764838#frequency_tab" }, { "id": "rs750764838", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750764838" }, { "id": "rs750764838", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750764838" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "5", "chr_pos": "10239194", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T60", "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" ] }, { "evidence": [ { "id": "Q6P4H8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->R).", "chr_id": "5", "chr_pos": "10239194", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T60", "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": "60", "end_pos": "60" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q6P4H8-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6P4H8-1.65.65", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q6P4H8-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "Q6P4H8-1", "length": 233, "uniprot_id": "ACKMT_HUMAN", "protein_name": "ATP synthase subunit C lysine N-methyltransferase", "refseq_ac": "NP_001245317", "refseq_name": "ATP synthase subunit C lysine N-methyltransferase isoform 2", "gene_name": "ATPSCKMT", "gene_names_uniprotkb": "ATPSCKMT; FAM173B", "gene_names_refseq": "ATPSCKMT; FAM173B; JS-2; hFAM173B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Lysine methylation by the mitochondrial methyltransferase FAM173B optimizes the function of mitochondrial ATP synthase.", "journal": "The Journal of biological chemistry", "date": "2019", "authors": "Malecki JM, Willemen HLDM, Pinto R, Ho AYY, Moen A, Kjonstad IF, Burgering BMT, Zwartkruis F, Eijkelkamp N, Falnes PO", "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" }, { "database": "RefSeq", "id": "NP_001245317", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001245317" } ], "reference": [ { "type": "PubMed", "id": "30530489", "url": "https://glygen.org/publication/PubMed/30530489" } ] } ], "crossref": [ { "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30530489", "url": "https://glygen.org/publication/PubMed/30530489", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SGDGRIVIAAAKKGFTAVGY", "down_seq": "LNPWLVWYSRYRAWREGVHG", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Abolished protein-lysine N-methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" }, { "database": "PubMed", "id": "30530489", "url": "https://glygen.org/publication/PubMed/30530489" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "60", "end_pos": "60" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6P4H8-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q6P4H8-1.102.102", "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": "Q6P4H8-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "Q6P4H8-1", "length": 233, "uniprot_id": "ACKMT_HUMAN", "protein_name": "ATP synthase subunit C lysine N-methyltransferase", "refseq_ac": "NP_001245317", "refseq_name": "ATP synthase subunit C lysine N-methyltransferase isoform 2", "gene_name": "ATPSCKMT", "gene_names_uniprotkb": "ATPSCKMT; FAM173B", "gene_names_refseq": "ATPSCKMT; FAM173B; JS-2; hFAM173B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of FAM173B as a protein methyltransferase promoting chronic pain.", "journal": "PLoS biology", "date": "2018", "authors": "Willemen HLDM, Kavelaars A, Prado J, Maas M, Versteeg S, Nellissen LJJ, Tromp J, Gonzalez Cano R, Zhou W, Jakobsson ME, Malecki J, Posthuma G, Habib AM, Heijnen CJ, Falnes PO, Eijkelkamp N", "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" }, { "database": "RefSeq", "id": "NP_001245317", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001245317" } ], "reference": [ { "type": "PubMed", "id": "29444090", "url": "https://glygen.org/publication/PubMed/29444090" } ] } ], "crossref": [ { "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "29444090", "url": "https://glygen.org/publication/PubMed/29444090", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TTKQIENVVKMLRCRRGSLV", "down_seq": "IGSGDGRIVIAAAKKGFTAV", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolished protein-lysine N-methyltransferase activity and ability to promote chronic pain.", "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" }, { "database": "PubMed", "id": "29444090", "url": "https://glygen.org/publication/PubMed/29444090" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "60", "end_pos": "60" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6P4H8-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6P4H8-1.102.102", "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": "Q6P4H8-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "Q6P4H8-1", "length": 233, "uniprot_id": "ACKMT_HUMAN", "protein_name": "ATP synthase subunit C lysine N-methyltransferase", "refseq_ac": "NP_001245317", "refseq_name": "ATP synthase subunit C lysine N-methyltransferase isoform 2", "gene_name": "ATPSCKMT", "gene_names_uniprotkb": "ATPSCKMT; FAM173B", "gene_names_refseq": "ATPSCKMT; FAM173B; JS-2; hFAM173B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P4H8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VVKMLRCRRGSLVDIGSGDG", "down_seq": "IVIAAAKKGFTAVGYELNPW", "snv": [ { "evidence": [ { "id": "Q6P4H8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8" } ], "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 (7).", "chr_id": "5", "chr_pos": "10239071", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R101", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "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: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": "60", "end_pos": "60" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6P4H8-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6P4H8-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6P4H8-1.117.117", "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": "Q6P4H8-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "Q6P4H8-1", "length": 233, "uniprot_id": "ACKMT_HUMAN", "protein_name": "ATP synthase subunit C lysine N-methyltransferase", "refseq_ac": "NP_001245317", "refseq_name": "ATP synthase subunit C lysine N-methyltransferase isoform 2", "gene_name": "ATPSCKMT", "gene_names_uniprotkb": "ATPSCKMT; FAM173B", "gene_names_refseq": "ATPSCKMT; FAM173B; JS-2; hFAM173B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P4H8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "VKMLRCRRGSLVDIGSGDGR", "down_seq": "VIAAAKKGFTAVGYELNPWL", "snv": [ { "evidence": [ { "id": "Q6P4H8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "10239068", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I102", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "60", "end_pos": "60" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6P4H8-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6P4H8-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6P4H8-1.117.117", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P4H8-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "Q6P4H8-1", "length": 233, "uniprot_id": "ACKMT_HUMAN", "protein_name": "ATP synthase subunit C lysine N-methyltransferase", "refseq_ac": "NP_001245317", "refseq_name": "ATP synthase subunit C lysine N-methyltransferase isoform 2", "gene_name": "ATPSCKMT", "gene_names_uniprotkb": "ATPSCKMT; FAM173B", "gene_names_refseq": "ATPSCKMT; FAM173B; JS-2; hFAM173B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6P4H8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VGGTLVAVYAVATPFVTPAL", "down_seq": "KVCLPFVPATTKQIENVVKM", "snv": [ { "evidence": [ { "id": "Q6P4H8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6P4H8" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "10239182", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R64", "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": "60", "end_pos": "60" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q6P4H8-1.60.60", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6P4H8-1.65.65", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6P4H8-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "Q6P4H8-1", "length": 233, "uniprot_id": "ACKMT_HUMAN", "protein_name": "ATP synthase subunit C lysine N-methyltransferase", "refseq_ac": "NP_001245317", "refseq_name": "ATP synthase subunit C lysine N-methyltransferase isoform 2", "gene_name": "ATPSCKMT", "gene_names_uniprotkb": "ATPSCKMT; FAM173B", "gene_names_refseq": "ATPSCKMT; FAM173B; JS-2; hFAM173B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6P4H8", "url": "https://www.uniprot.org/uniprotkb/Q6P4H8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1379482389", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1379482389", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1379482389", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1379482389#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1379482389", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1379482389", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GGTLVAVYAVATPFVTPALR", "down_seq": "VCLPFVPATTKQIENVVKML", "snv": [ { "evidence": [ { "id": "rs1379482389", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1379482389" }, { "id": "rs1379482389", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1379482389#frequency_tab" }, { "id": "rs1379482389", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1379482389" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KVC->NVC).", "chr_id": "5", "chr_pos": "10239178", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K65", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "60", "end_pos": "60" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q6P4H8-1.60.60", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6P4H8-1.64.64", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78346-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P78346-1", "length": 268, "uniprot_id": "RPP30_HUMAN", "protein_name": "Ribonuclease P protein subunit p30", "refseq_ac": "NP_001098016", "refseq_name": "ribonuclease P protein subunit p30 isoform a", "gene_name": "RPP30", "gene_names_uniprotkb": "RPP30; RNASEP2", "gene_names_refseq": "RPP30; TSG15", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P78346", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P78346" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P78346", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P78346" } ], "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": "P78346", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P78346" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P78346", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P78346", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "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": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "P78346", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P78346" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "85", "end_pos": "85" } ] } ], "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": "P78346-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "P78346-1", "length": 268, "uniprot_id": "RPP30_HUMAN", "protein_name": "Ribonuclease P protein subunit p30", "refseq_ac": "NP_001098016", "refseq_name": "ribonuclease P protein subunit p30 isoform a", "gene_name": "RPP30", "gene_names_uniprotkb": "RPP30; RNASEP2", "gene_names_refseq": "RPP30; TSG15", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" } ], "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": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346", "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": "TNCRAALLHGETRKTAFGII", "down_seq": "TVKKPRPSEGDEDCLPASKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "85", "end_pos": "85" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P78346-1.244.244", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P78346-1.251.251", "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": "P78346-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "P78346-1", "length": 268, "uniprot_id": "RPP30_HUMAN", "protein_name": "Ribonuclease P protein subunit p30", "refseq_ac": "NP_001098016", "refseq_name": "ribonuclease P protein subunit p30 isoform a", "gene_name": "RPP30", "gene_names_uniprotkb": "RPP30; RNASEP2", "gene_names_refseq": "RPP30; TSG15", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" } ], "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": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346", "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": "NCRAALLHGETRKTAFGIIS", "down_seq": "VKKPRPSEGDEDCLPASKKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr244" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "85", "end_pos": "85" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P78346-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P78346-1.251.251", "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": "P78346-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "P78346-1", "length": 268, "uniprot_id": "RPP30_HUMAN", "protein_name": "Ribonuclease P protein subunit p30", "refseq_ac": "NP_001098016", "refseq_name": "ribonuclease P protein subunit p30 isoform a", "gene_name": "RPP30", "gene_names_uniprotkb": "RPP30; RNASEP2", "gene_names_refseq": "RPP30; TSG15", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" } ], "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": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" }, { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis.", "journal": "Journal of proteome research", "date": "2008", "authors": "Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd", "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" }, { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" } ], "reference": [ { "type": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" } ] }, { "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": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" }, { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" }, { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" }, { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "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": "HGETRKTAFGIISTVKKPRP", "down_seq": "EGDEDCLPASKKAKCEG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser251" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "85", "end_pos": "85" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P78346-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P78346-1.244.244", "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": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78346-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P78346-1", "length": 268, "uniprot_id": "RPP30_HUMAN", "protein_name": "Ribonuclease P protein subunit p30", "refseq_ac": "NP_001098016", "refseq_name": "ribonuclease P protein subunit p30 isoform a", "gene_name": "RPP30", "gene_names_uniprotkb": "RPP30; RNASEP2", "gene_names_refseq": "RPP30; TSG15", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" } ], "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": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346", "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": "FTTLPIVQGKSRPIKILTRL", "down_seq": "IIVSDPSHCNVLRATSSRAR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr78" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "85", "end_pos": "85" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P78346-1.85.85", "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": "P78346-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "P78346-1", "length": 268, "uniprot_id": "RPP30_HUMAN", "protein_name": "Ribonuclease P protein subunit p30", "refseq_ac": "NP_001098016", "refseq_name": "ribonuclease P protein subunit p30 isoform a", "gene_name": "RPP30", "gene_names_uniprotkb": "RPP30; RNASEP2", "gene_names_refseq": "RPP30; TSG15", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78346", "url": "https://www.uniprot.org/uniprotkb/P78346" } ], "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": "P78346-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346", "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": "QGKSRPIKILTRLTIIVSDP", "down_seq": "HCNVLRATSSRARLYDVVAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P78346", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78346" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser85" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "85", "end_pos": "85" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P78346-1.78.78", "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": "Q8WVB3-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "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": "rs1369455100", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369455100", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1369455100", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369455100", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754273625", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754273625", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754273625", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754273625", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754273625", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754273625#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754273625", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754273625", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754273625", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754273625", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PVEHHLRNHVQWLQVAGSGP", "down_seq": "DSLQGIILTGWQRYDHYSVL", "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": "Thr287", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1369455100", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369455100" }, { "id": "rs1369455100", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369455100" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82437323", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T287", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs754273625", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754273625" }, { "id": "rs754273625", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754273625" }, { "id": "rs754273625", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754273625#frequency_tab" }, { "id": "rs754273625", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754273625" }, { "id": "rs754273625", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754273625" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 2 filters: o-glyco-site-loss (T->M); glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82437324", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T287", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.306.306", "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": "Q8WVB3-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of Human Nucleocytoplasmic Hexosaminidase D.", "journal": "Biochemistry", "date": "2016", "authors": "Alteen MG, Oehler V, Nemcovicova I, Wilson IB, Vocadlo DJ, Gloster TM", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "RefSeq", "id": "NP_001317471", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001317471" } ], "reference": [ { "type": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] } ], "crossref": [ { "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AMIDQVLELHPGAQRLHIGC", "down_seq": "EVYYLGEGEASRRWLQQEQN", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Loss of hexosaminidase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] }, { "sequence_org": "D", "sequence_mut": "N", "comment": "Loss of hexosaminidase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.149.149", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.168.168", "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": "Q8WVB3-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of Human Nucleocytoplasmic Hexosaminidase D.", "journal": "Biochemistry", "date": "2016", "authors": "Alteen MG, Oehler V, Nemcovicova I, Wilson IB, Vocadlo DJ, Gloster TM", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "RefSeq", "id": "NP_001317471", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001317471" } ], "reference": [ { "type": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] } ], "crossref": [ { "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1205869711", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205869711", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1205869711", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1205869711#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1205869711", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205869711", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MIDQVLELHPGAQRLHIGCD", "down_seq": "VYYLGEGEASRRWLQQEQNS", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Decreases hexosaminidase activity. Optimum pH shifts to 7.5.", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] }, { "sequence_org": "E", "sequence_mut": "N", "comment": "Decreases hexosaminidase activity. Optimum pH shifts to 7.5.", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] } ], "snv": [ { "evidence": [ { "id": "rs1205869711", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205869711" }, { "id": "rs1205869711", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1205869711#frequency_tab" }, { "id": "rs1205869711", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205869711" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82433822", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E149", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.148.148", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.169.169", "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": "Q8WVB3-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mechanism of Human Nucleocytoplasmic Hexosaminidase D.", "journal": "Biochemistry", "date": "2016", "authors": "Alteen MG, Oehler V, Nemcovicova I, Wilson IB, Vocadlo DJ, Gloster TM", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "RefSeq", "id": "NP_001317471", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001317471" } ], "reference": [ { "type": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] } ], "crossref": [ { "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "ILHLAGLNELEVIPLVQTFG", "down_seq": "MEFVLKHTAFAHLREVGSFP", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Decreases hexosaminidase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" }, { "database": "PubMed", "id": "27149221", "url": "https://glygen.org/publication/PubMed/27149221" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.112.112", "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": "Q8WVB3-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs4789773", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs4789773", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4789773", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs4789773", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs4789773", "url": "https://www.ncbi.nlm.nih.gov/snp/rs4789773#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs4789773", "url": "http://gnomad.broadinstitute.org/awesome?query=rs4789773", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs4789773", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4789773", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs755432793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755432793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755432793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755432793", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755432793", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755432793#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755432793", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755432793", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LVGAMIDQVLELHPGAQRLH", "down_seq": "GCDEVYYLGEGEASRRWLQQ", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs4789773", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773" }, { "id": "rs4789773", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4789773" }, { "id": "rs4789773", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773" }, { "id": "rs4789773", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs4789773#frequency_tab" }, { "id": "rs4789773", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs4789773" }, { "id": "rs4789773", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4789773" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "12", "frequency": "0.3", "sequence_org": "I", "sequence_mut": "V", "comment": "Somatic mutation passed 2 filters: patient count (12/4799); protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82433808", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "I145", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs4789773", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773" }, { "id": "rs4789773", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4789773" }, { "id": "rs4789773", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773" }, { "id": "rs4789773", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs4789773#frequency_tab" }, { "id": "rs4789773", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs4789773" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82433808", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs4789773", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773" }, { "id": "rs4789773", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4789773" }, { "id": "rs4789773", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4789773" }, { "id": "rs4789773", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs4789773#frequency_tab" }, { "id": "rs4789773", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs4789773" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82433808", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755432793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755432793" }, { "id": "rs755432793", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755432793" }, { "id": "rs755432793", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755432793#frequency_tab" }, { "id": "rs755432793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755432793" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82433810", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.148.148", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.149.149", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.165.165", "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": 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": "Q8WVB3-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs749879786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749879786", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749879786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749879786", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749879786", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749879786#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749879786", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749879786", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs749879786", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs749879786", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs767055141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767055141", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767055141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767055141", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767055141", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767055141#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs767055141", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767055141", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VYYLGEGEASRRWLQQEQNS", "down_seq": "GKLCLSHMRAVASGVKARRP", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs749879786", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749879786" }, { "id": "rs749879786", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749879786" }, { "id": "rs749879786", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749879786#frequency_tab" }, { "id": "rs749879786", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749879786" }, { "id": "rs749879786", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs749879786" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82435750", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T170", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs767055141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767055141" }, { "id": "rs767055141", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767055141" }, { "id": "rs767055141", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767055141#frequency_tab" }, { "id": "rs767055141", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767055141" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435749", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T170", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749879786", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749879786" }, { "id": "rs749879786", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749879786" }, { "id": "rs749879786", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749879786#frequency_tab" }, { "id": "rs749879786", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749879786" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435750", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T170", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.190.190", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "Q8WVB3-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1293987698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1293987698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1293987698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1293987698", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754837257", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754837257", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754837257", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754837257", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754837257", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754837257#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754837257", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754837257", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "YLGEGEASRRWLQQEQNSTG", "down_seq": "LCLSHMRAVASGVKARRPSV", "snv": [ { "evidence": [ { "id": "rs1293987698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1293987698" }, { "id": "rs1293987698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1293987698" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (KLC->NLC); glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435757", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs754837257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754837257" }, { "id": "rs754837257", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754837257" }, { "id": "rs754837257", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754837257#frequency_tab" }, { "id": "rs754837257", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754837257" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435756", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs754837257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754837257" }, { "id": "rs754837257", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754837257" }, { "id": "rs754837257", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754837257#frequency_tab" }, { "id": "rs754837257", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754837257" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435756", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.192.192", "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": 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": "Q8WVB3-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs112909670", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs112909670", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs112909670", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs112909670", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs112909670", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs112909670", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs112909670", "url": "https://www.ncbi.nlm.nih.gov/snp/rs112909670#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs112909670", "url": "http://gnomad.broadinstitute.org/awesome?query=rs112909670", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs112909670", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs112909670", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs771002436", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771002436", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771002436", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771002436", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771002436", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771002436#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771002436", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771002436", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SRRWLQQEQNSTGKLCLSHM", "down_seq": "AVASGVKARRPSVTPLVWDD", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs112909670", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs112909670" }, { "id": "rs112909670", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs112909670" }, { "id": "rs112909670", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs112909670" }, { "id": "rs112909670", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs112909670#frequency_tab" }, { "id": "rs112909670", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs112909670" }, { "id": "rs112909670", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs112909670" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82435776", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R179", "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", "ebi" ] }, { "evidence": [ { "id": "rs771002436", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771002436" }, { "id": "rs771002436", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771002436" }, { "id": "rs771002436", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771002436#frequency_tab" }, { "id": "rs771002436", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771002436" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435777", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R179", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.161.161", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.199.199", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "Q8WVB3-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201473179", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201473179", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201473179", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201473179", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201473179", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201473179", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201473179", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201473179#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201473179", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201473179", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201473179", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201473179", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs777599293", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777599293", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777599293", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777599293", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777599293", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777599293#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777599293", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777599293", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "STGKLCLSHMRAVASGVKAR", "down_seq": "PSVTPLVWDDMLRDLPEDQL", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs201473179", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201473179" }, { "id": "rs201473179", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201473179" }, { "id": "rs201473179", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201473179" }, { "id": "rs201473179", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201473179#frequency_tab" }, { "id": "rs201473179", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201473179" }, { "id": "rs201473179", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201473179" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 2 filters: num. of cancers (4); protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82435807", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R189", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs777599293", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777599293" }, { "id": "rs777599293", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777599293" }, { "id": "rs777599293", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777599293#frequency_tab" }, { "id": "rs777599293", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777599293" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82435806", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R189", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.208.208", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "Q8WVB3-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs375790128", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375790128", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375790128", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375790128", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375790128", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375790128#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs375790128", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375790128", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GKLCLSHMRAVASGVKARRP", "down_seq": "VTPLVWDDMLRDLPEDQLAA", "snv": [ { "evidence": [ { "id": "rs375790128", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375790128" }, { "id": "rs375790128", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375790128" }, { "id": "rs375790128", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375790128#frequency_tab" }, { "id": "rs375790128", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375790128" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (SVT->NVT); glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435813", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S191", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs375790128", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375790128" }, { "id": "rs375790128", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375790128" }, { "id": "rs375790128", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375790128#frequency_tab" }, { "id": "rs375790128", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375790128" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435813", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S191", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.211.211", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8WVB3-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs774736554", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774736554", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774736554", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774736554", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774736554", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774736554#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774736554", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774736554", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs774736554", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774736554", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs748678762", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748678762", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748678762", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748678762", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748678762", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748678762#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748678762", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748678762", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ASGVKARRPSVTPLVWDDML", "down_seq": "DLPEDQLAASGVPQLVEPVL", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs774736554", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774736554" }, { "id": "rs774736554", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774736554" }, { "id": "rs774736554", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774736554#frequency_tab" }, { "id": "rs774736554", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774736554" }, { "id": "rs774736554", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774736554" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82435845", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R202", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs748678762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748678762" }, { "id": "rs748678762", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748678762" }, { "id": "rs748678762", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748678762#frequency_tab" }, { "id": "rs748678762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748678762" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435846", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R202", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748678762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748678762" }, { "id": "rs748678762", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748678762" }, { "id": "rs748678762", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748678762#frequency_tab" }, { "id": "rs748678762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748678762" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82435846", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R202", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.222.222", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q8WVB3-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs935436582", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs935436582", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs935436582", "url": "https://www.ensembl.org/id/rs935436582", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs758665792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758665792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758665792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758665792", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758665792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758665792", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VTQVSLHLRSSVDALLEGNR", "down_seq": "VTGWFSPYHRQRKLIHPVMV", "snv": [ { "evidence": [ { "id": "rs935436582", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs935436582" }, { "id": "rs935436582", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs935436582" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NRY->NRC); glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82441802", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y389", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758665792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758665792" }, { "id": "rs758665792", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758665792" }, { "id": "rs758665792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758665792" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82441801", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y389", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.370.370", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.399.399", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.408.408", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.409.409", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q8WVB3-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1249401166", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249401166", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1249401166", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1249401166#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1249401166", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249401166", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1383659606", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1383659606", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1383659606", "url": "https://www.ensembl.org/id/rs1383659606", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PPKVSYLSEIFPLFRALGAN", "down_seq": "LLIEYEDMFPYEGPLRLLRA", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82424427", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G40", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-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": "rs1249401166", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249401166" }, { "id": "rs1249401166", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1249401166#frequency_tab" }, { "id": "rs1249401166", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249401166" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82424427", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G40", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1383659606", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1383659606" }, { "id": "rs1383659606", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1383659606" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82424428", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G40", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.60.60", "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": 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": "Q8WVB3-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2053676329", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2053676329", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2053676329", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2053676329", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LNELEVIPLVQTFGHMEFVL", "down_seq": "HTAFAHLREVGSFPCTLNPH", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-gain (KHT->NHT); protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82433669", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K98", "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": "rs2053676329", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2053676329" }, { "id": "rs2053676329", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2053676329" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82433668", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K98", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.92.92", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WVB3-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.117.117", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WVB3-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201899631", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201899631", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201899631", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201899631", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201899631", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201899631#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201899631", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201899631", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201899631", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201899631", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ELEVIPLVQTFGHMEFVLKH", "down_seq": "AFAHLREVGSFPCTLNPHEA", "snv": [ { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs201899631", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201899631" }, { "id": "rs201899631", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201899631" }, { "id": "rs201899631", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201899631#frequency_tab" }, { "id": "rs201899631", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201899631" }, { "id": "rs201899631", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201899631" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82433674", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T100", "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": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.92.92", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WVB3-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WVB3-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.119.119", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WVB3-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs188244152", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188244152", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs188244152", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188244152", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs188244152", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188244152", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs188244152", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188244152#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs188244152", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188244152", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8WVB3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VIPLVQTFGHMEFVLKHTAF", "down_seq": "HLREVGSFPCTLNPHEAESL", "snv": [ { "evidence": [ { "id": "rs188244152", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188244152" }, { "id": "rs188244152", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188244152" }, { "id": "rs188244152", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188244152" }, { "id": "rs188244152", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188244152#frequency_tab" }, { "id": "rs188244152", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188244152" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82433682", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "A103", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8WVB3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WVB3" }, { "id": "rs188244152", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188244152" }, { "id": "rs188244152", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188244152" }, { "id": "rs188244152", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188244152" }, { "id": "rs188244152", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188244152#frequency_tab" }, { "id": "rs188244152", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188244152" } ], "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, glycosylhydrolase).", "chr_id": "17", "chr_pos": "82433682", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A103", "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": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WVB3-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.92.92", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WVB3-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WVB3-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WVB3-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WVB3-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WVB3-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WVB3-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WVB3-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WVB3-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WVB3-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WVB3-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "Q8WVB3-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "Q8WVB3-1", "length": 486, "uniprot_id": "HEXD_HUMAN", "protein_name": "Hexosaminidase D", "refseq_ac": "NP_001317471", "refseq_name": "hexosaminidase D isoform 2", "gene_name": "HEXD", "gene_names_uniprotkb": "HEXD; HEXDC", "gene_names_refseq": "HEXDC; HEXD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WVB3", "url": "https://www.uniprot.org/uniprotkb/Q8WVB3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759509250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759509250", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759509250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759509250", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759509250", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759509250", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IPLVQTFGHMEFVLKHTAFA", "down_seq": "LREVGSFPCTLNPHEAESLA", "snv": [ { "evidence": [ { "id": "rs759509250", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759509250" }, { "id": "rs759509250", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759509250" }, { "id": "rs759509250", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759509250" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, glycosylhydrolase.", "chr_id": "17", "chr_pos": "82433685", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "145", "end_pos": "145" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "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": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "150", "end_pos": "150" }, { "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": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "484", "end_pos": "484" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "48", "end_pos": "48" }, { "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": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WVB3-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8WVB3-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WVB3-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WVB3-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8WVB3-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WVB3-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WVB3-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WVB3-1.92.92", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WVB3-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WVB3-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WVB3-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WVB3-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WVB3-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WVB3-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WVB3-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WVB3-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WVB3-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WVB3-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WVB3-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WVB3-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WVB3-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WVB3-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WVB3-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WVB3-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WVB3-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WVB3-1.124.124", "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": [] } ] } ]