{ "batchid": 2, "recordid": "P22105-3", "recordtype": "protein", "sections": { "snv": [ { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 110, "end_pos": 110, "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097870", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L110", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1110, "end_pos": 1110, "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084530", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1110", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2483692679", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483692679" } ], "glycoeffect": [], "start_pos": 1110, "end_pos": 1110, "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084529", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1110", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs1779657498", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779657498" }, { "id": "rs1779657498", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779657498#frequency_tab" }, { "id": "rs1779657498", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779657498" }, { "id": "rs1779657498", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779657498" } ], "glycoeffect": [], "start_pos": 1111, "end_pos": 1111, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084526", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1111", "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": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1111, "end_pos": 1111, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084527", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1111", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs751770127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751770127" }, { "id": "rs751770127", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751770127" }, { "id": "rs751770127", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751770127#frequency_tab" }, { "id": "rs751770127", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751770127" } ], "glycoeffect": [], "start_pos": 1111, "end_pos": 1111, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084527", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1111", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1452792297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452792297" }, { "id": "rs1452792297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452792297" } ], "glycoeffect": [], "start_pos": 1112, "end_pos": 1112, "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084523", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1112", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs367775946", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367775946" }, { "id": "rs367775946", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs367775946#frequency_tab" }, { "id": "rs367775946", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367775946" } ], "glycoeffect": [], "start_pos": 1113, "end_pos": 1113, "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084521", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1113", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs764270756", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764270756" }, { "id": "rs764270756", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764270756" }, { "id": "rs764270756", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764270756#frequency_tab" }, { "id": "rs764270756", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764270756" } ], "glycoeffect": [], "start_pos": 1113, "end_pos": 1113, "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084520", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1113", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764270756", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764270756" }, { "id": "rs764270756", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764270756" }, { "id": "rs764270756", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764270756#frequency_tab" }, { "id": "rs764270756", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764270756" } ], "glycoeffect": [], "start_pos": 1113, "end_pos": 1113, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084520", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1113", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758509219", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758509219" }, { "id": "rs758509219", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758509219" }, { "id": "rs758509219", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758509219#frequency_tab" }, { "id": "rs758509219", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758509219" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1114, "end_pos": 1114, "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084517", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1114", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1562857100", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1562857100" }, { "id": "rs1562857100", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1562857100" } ], "glycoeffect": [], "start_pos": 1115, "end_pos": 1115, "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084515", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1115", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1115, "end_pos": 1115, "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084515", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1115", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs760558082", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760558082" }, { "id": "rs760558082", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760558082" }, { "id": "rs760558082", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760558082#frequency_tab" }, { "id": "rs760558082", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760558082" } ], "glycoeffect": [], "start_pos": 1116, "end_pos": 1116, "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084512", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760558082", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760558082" }, { "id": "rs760558082", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760558082" }, { "id": "rs760558082", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760558082#frequency_tab" }, { "id": "rs760558082", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760558082" } ], "glycoeffect": [], "start_pos": 1116, "end_pos": 1116, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084512", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1206170488", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1206170488" }, { "id": "rs1206170488", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1206170488" } ], "glycoeffect": [], "start_pos": 1117, "end_pos": 1117, "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084509", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1117", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1119, "end_pos": 1119, "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084502", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1119", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1780499321", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780499321" }, { "id": "rs1780499321", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1780499321#frequency_tab" } ], "glycoeffect": [], "start_pos": 111, "end_pos": 111, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097868", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E111", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1780499321", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780499321" }, { "id": "rs1780499321", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1780499321#frequency_tab" } ], "glycoeffect": [], "start_pos": 111, "end_pos": 111, "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097868", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E111", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs373648686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373648686" }, { "id": "rs373648686", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373648686" }, { "id": "rs373648686", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373648686" }, { "id": "rs373648686", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373648686" } ], "glycoeffect": [], "start_pos": 1124, "end_pos": 1124, "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084488", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1124", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs773928791", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773928791" }, { "id": "rs773928791", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773928791" }, { "id": "rs773928791", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773928791" }, { "id": "rs773928791", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773928791" } ], "glycoeffect": [], "start_pos": 1124, "end_pos": 1124, "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084487", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1124", "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": "rs61910712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61910712" }, { "id": "rs61910712", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61910712" }, { "id": "rs61910712", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61910712" }, { "id": "rs61910712", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61910712#frequency_tab" }, { "id": "rs61910712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61910712" } ], "glycoeffect": [], "start_pos": 1127, "end_pos": 1127, "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084478", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.0196232", "site_lbl": "K1127", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 112, "end_pos": 112, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097865", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E112", "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": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 112, "end_pos": 112, "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097865", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "E112", "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": "rs1328204527", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328204527" }, { "id": "rs1328204527", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1328204527" } ], "glycoeffect": [], "start_pos": 1130, "end_pos": 1130, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084469", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1130", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768297553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768297553" }, { "id": "rs768297553", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs768297553" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1131, "end_pos": 1131, "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084466", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1131", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779652525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779652525" }, { "id": "rs1779652525", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779652525#frequency_tab" }, { "id": "rs1779652525", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779652525" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1131, "end_pos": 1131, "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084467", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1131", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1132, "end_pos": 1132, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084463", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1132", "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": "rs1349938512", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349938512" }, { "id": "rs1349938512", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349938512#frequency_tab" }, { "id": "rs1349938512", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349938512" } ], "glycoeffect": [], "start_pos": 1132, "end_pos": 1132, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084464", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1132", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs1349938512", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349938512" }, { "id": "rs1349938512", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349938512#frequency_tab" }, { "id": "rs1349938512", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349938512" } ], "glycoeffect": [], "start_pos": 1132, "end_pos": 1132, "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084464", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G1132", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1381525491", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381525491" }, { "id": "rs1381525491", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381525491" } ], "glycoeffect": [], "start_pos": 1134, "end_pos": 1134, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084458", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1134", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779651392", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779651392" }, { "id": "rs1779651392", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779651392#frequency_tab" } ], "glycoeffect": [], "start_pos": 1135, "end_pos": 1135, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084455", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1135", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1285395327", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1285395327" }, { "id": "rs1285395327", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1285395327#frequency_tab" }, { "id": "rs1285395327", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1285395327" } ], "glycoeffect": [], "start_pos": 1136, "end_pos": 1136, "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084451", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770173982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770173982" }, { "id": "rs770173982", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770173982" }, { "id": "rs770173982", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770173982" } ], "glycoeffect": [], "start_pos": 1137, "end_pos": 1137, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084449", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1137", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483691715", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483691715" } ], "glycoeffect": [], "start_pos": 1138, "end_pos": 1138, "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084444", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1138", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746315834", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746315834" }, { "id": "rs746315834", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746315834" }, { "id": "rs746315834", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746315834#frequency_tab" }, { "id": "rs746315834", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746315834" } ], "glycoeffect": [], "start_pos": 1139, "end_pos": 1139, "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084442", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1139", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs149995364", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149995364" }, { "id": "rs149995364", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149995364" }, { "id": "rs149995364", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149995364" }, { "id": "rs149995364", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149995364#frequency_tab" }, { "id": "rs149995364", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149995364" }, { "id": "rs149995364", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149995364" } ], "glycoeffect": [], "start_pos": 1140, "end_pos": 1140, "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "NC_000006.12", "chr_pos": "32084439", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "0.00879", "site_lbl": "G1140", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1140, "end_pos": 1140, "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084439", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1140", "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" ] }, { "evidence": [ { "id": "rs1435025447", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435025447" }, { "id": "rs1435025447", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435025447" } ], "glycoeffect": [], "start_pos": 1140, "end_pos": 1140, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084440", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1140", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs771352294", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771352294" }, { "id": "rs771352294", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771352294" }, { "id": "rs771352294", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771352294#frequency_tab" }, { "id": "rs771352294", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771352294" }, { "id": "rs771352294", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771352294" } ], "glycoeffect": [], "start_pos": 1141, "end_pos": 1141, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084436", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1141", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1141, "end_pos": 1141, "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084437", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1141", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs965570472", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs965570472" }, { "id": "rs965570472", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs965570472#frequency_tab" }, { "id": "rs965570472", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs965570472" } ], "glycoeffect": [], "start_pos": 1143, "end_pos": 1143, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084431", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1143", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779648914", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779648914" }, { "id": "rs1779648914", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779648914#frequency_tab" }, { "id": "rs1779648914", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779648914" } ], "glycoeffect": [], "start_pos": 1146, "end_pos": 1146, "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084421", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1146", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1194548088", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194548088" }, { "id": "rs1194548088", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194548088" } ], "glycoeffect": [], "start_pos": 1146, "end_pos": 1146, "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084422", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1146", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1194548088", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194548088" }, { "id": "rs1194548088", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194548088" } ], "glycoeffect": [], "start_pos": 1146, "end_pos": 1146, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32084422", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1146", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1147, "end_pos": 1147, "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32084417", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1147", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs769286386", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769286386" }, { "id": "rs769286386", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769286386" }, { "id": "rs769286386", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769286386" } ], "glycoeffect": [], "start_pos": 1150, "end_pos": 1150, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082324", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1150", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483679351", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483679351" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1152, "end_pos": 1152, "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082317", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1152", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1439741377", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439741377" }, { "id": "rs1439741377", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1439741377" } ], "glycoeffect": [], "start_pos": 1154, "end_pos": 1154, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082312", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1154", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1046927909", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1046927909" }, { "id": "rs1046927909", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1046927909" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1155, "end_pos": 1155, "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082309", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1155", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483679222", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483679222" } ], "glycoeffect": [], "start_pos": 1155, "end_pos": 1155, "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082308", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1155", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779515414", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779515414" }, { "id": "rs1779515414", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779515414" } ], "glycoeffect": [], "start_pos": 1156, "end_pos": 1156, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082306", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1156", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759962141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759962141" }, { "id": "rs759962141", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759962141" }, { "id": "rs759962141", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759962141" }, { "id": "rs759962141", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs759962141" } ], "glycoeffect": [], "start_pos": 1157, "end_pos": 1157, "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082303", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1157", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779514755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779514755" } ], "glycoeffect": [], "start_pos": 1159, "end_pos": 1159, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082297", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1159", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777234685", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777234685" }, { "id": "rs777234685", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777234685" }, { "id": "rs777234685", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777234685" } ], "glycoeffect": [], "start_pos": 1159, "end_pos": 1159, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082296", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1159", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779514755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779514755" }, { "id": "rs1779514755", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779514755#frequency_tab" }, { "id": "rs1779514755", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779514755" } ], "glycoeffect": [], "start_pos": 1159, "end_pos": 1159, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082297", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1159", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs185819", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185819" }, { "id": "rs185819", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs185819" }, { "id": "rs185819", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185819" }, { "id": "rs185819", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs185819#frequency_tab" }, { "id": "rs185819", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs185819" } ], "glycoeffect": [], "start_pos": 1161, "end_pos": 1161, "sequence_org": "H", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082290", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1161", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs903196142", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs903196142" }, { "id": "rs903196142", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs903196142#frequency_tab" }, { "id": "rs903196142", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs903196142" } ], "glycoeffect": [], "start_pos": 1161, "end_pos": 1161, "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082291", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1161", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs185819", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185819" }, { "id": "rs185819", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs185819" }, { "id": "rs185819", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185819" }, { "id": "rs185819", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs185819#frequency_tab" }, { "id": "rs185819", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs185819" }, { "id": "rs185819", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs185819" } ], "glycoeffect": [], "start_pos": 1161, "end_pos": 1161, "sequence_org": "H", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082290", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1161", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs185819", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185819" }, { "id": "rs185819", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs185819" }, { "id": "rs185819", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185819" }, { "id": "rs185819", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs185819#frequency_tab" }, { "id": "rs185819", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs185819" }, { "id": "rs185819", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs185819" } ], "glycoeffect": [], "start_pos": 1161, "end_pos": 1161, "sequence_org": "H", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082290", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1161", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs903196142", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs903196142" }, { "id": "rs903196142", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs903196142#frequency_tab" }, { "id": "rs903196142", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs903196142" } ], "glycoeffect": [], "start_pos": 1161, "end_pos": 1161, "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082291", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1161", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs185207099", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185207099" }, { "id": "rs185207099", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs185207099" }, { "id": "rs185207099", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs185207099" }, { "id": "rs185207099", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs185207099#frequency_tab" }, { "id": "rs185207099", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs185207099" }, { "id": "rs185207099", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs185207099" } ], "glycoeffect": [], "start_pos": 1163, "end_pos": 1163, "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082284", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1163", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs2127257051", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127257051" }, { "id": "rs2127257051", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127257051" } ], "glycoeffect": [], "start_pos": 1164, "end_pos": 1164, "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082282", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1164", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs914805218", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs914805218" }, { "id": "rs914805218", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs914805218#frequency_tab" } ], "glycoeffect": [], "start_pos": 1167, "end_pos": 1167, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082273", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1167", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127257036", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127257036" }, { "id": "rs2127257036", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127257036" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1168, "end_pos": 1168, "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082270", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1168", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127257031", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127257031" }, { "id": "rs2127257031", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127257031" } ], "glycoeffect": [], "start_pos": 1169, "end_pos": 1169, "sequence_org": "D", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082266", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1169", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772179236", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179236" }, { "id": "rs772179236", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772179236" }, { "id": "rs772179236", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772179236" } ], "glycoeffect": [], "start_pos": 1169, "end_pos": 1169, "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082265", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1169", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1216124530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216124530" }, { "id": "rs1216124530", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1216124530#frequency_tab" }, { "id": "rs1216124530", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216124530" } ], "glycoeffect": [], "start_pos": 116, "end_pos": 116, "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097852", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1216124530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216124530" }, { "id": "rs1216124530", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1216124530#frequency_tab" }, { "id": "rs1216124530", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216124530" } ], "glycoeffect": [], "start_pos": 116, "end_pos": 116, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097852", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1780499152", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780499152" }, { "id": "rs1780499152", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1780499152" } ], "glycoeffect": [], "start_pos": 116, "end_pos": 116, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097853", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1216124530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216124530" }, { "id": "rs1216124530", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1216124530#frequency_tab" }, { "id": "rs1216124530", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216124530" } ], "glycoeffect": [], "start_pos": 116, "end_pos": 116, "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097852", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1369354124", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369354124" }, { "id": "rs1369354124", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1369354124#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1171, "end_pos": 1171, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082260", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1171", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1463608673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463608673" }, { "id": "rs1463608673", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1463608673#frequency_tab" }, { "id": "rs1463608673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463608673" } ], "glycoeffect": [], "start_pos": 1172, "end_pos": 1172, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082258", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778873660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778873660" }, { "id": "rs778873660", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778873660" }, { "id": "rs778873660", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778873660#frequency_tab" }, { "id": "rs778873660", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778873660" } ], "glycoeffect": [], "start_pos": 1173, "end_pos": 1173, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082255", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1173", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779510121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779510121" }, { "id": "rs1779510121", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779510121" } ], "glycoeffect": [], "start_pos": 1176, "end_pos": 1176, "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082246", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1176", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1180471389", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1180471389" }, { "id": "rs1180471389", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1180471389" } ], "glycoeffect": [], "start_pos": 1177, "end_pos": 1177, "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082243", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1177", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1180471389", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1180471389" }, { "id": "rs1180471389", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1180471389" } ], "glycoeffect": [], "start_pos": 1177, "end_pos": 1177, "sequence_org": "L", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082243", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1177", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1471315134", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471315134" }, { "id": "rs1471315134", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471315134" } ], "glycoeffect": [], "start_pos": 1177, "end_pos": 1177, "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082242", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1177", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779509254", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779509254" }, { "id": "rs1779509254", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779509254" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1178, "end_pos": 1178, "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082239", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1178", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755019154", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755019154" }, { "id": "rs755019154", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755019154" }, { "id": "rs755019154", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755019154#frequency_tab" }, { "id": "rs755019154", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755019154" } ], "glycoeffect": [], "start_pos": 1179, "end_pos": 1179, "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082235", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W1179", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127256914", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127256914" }, { "id": "rs2127256914", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127256914" } ], "glycoeffect": [], "start_pos": 1180, "end_pos": 1180, "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082234", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1180", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779508775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779508775" }, { "id": "rs1779508775", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779508775#frequency_tab" } ], "glycoeffect": [], "start_pos": 1181, "end_pos": 1181, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082231", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1181", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs541777190", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs541777190" }, { "id": "rs541777190", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs541777190" }, { "id": "rs541777190", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs541777190" }, { "id": "rs541777190", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs541777190" }, { "id": "rs541777190", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs541777190" } ], "glycoeffect": [], "start_pos": 1182, "end_pos": 1182, "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082228", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.0002", "site_lbl": "P1182", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs757095620", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757095620" }, { "id": "rs757095620", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757095620" }, { "id": "rs757095620", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757095620#frequency_tab" }, { "id": "rs757095620", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757095620" } ], "glycoeffect": [], "start_pos": 1183, "end_pos": 1183, "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082223", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1183", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781061300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781061300" }, { "id": "rs781061300", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781061300" }, { "id": "rs781061300", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781061300" }, { "id": "rs781061300", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs781061300" } ], "glycoeffect": [], "start_pos": 1183, "end_pos": 1183, "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082225", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1183", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs113295126", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs113295126" }, { "id": "rs113295126", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs113295126" } ], "glycoeffect": [], "start_pos": 1186, "end_pos": 1186, "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082215", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1186", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779507551", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779507551" }, { "id": "rs1779507551", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779507551#frequency_tab" }, { "id": "rs1779507551", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779507551" }, { "id": "rs1779507551", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779507551" } ], "glycoeffect": [], "start_pos": 1186, "end_pos": 1186, "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082214", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1186", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1214298177", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1214298177" }, { "id": "rs1214298177", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1214298177#frequency_tab" }, { "id": "rs1214298177", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1214298177" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1188, "end_pos": 1188, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082209", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1188", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1214298177", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1214298177" }, { "id": "rs1214298177", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1214298177#frequency_tab" }, { "id": "rs1214298177", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1214298177" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1188, "end_pos": 1188, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082209", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1188", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1582442025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582442025" }, { "id": "rs1582442025", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1582442025" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1188, "end_pos": 1188, "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082210", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1188", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763877578", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763877578" }, { "id": "rs763877578", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763877578" }, { "id": "rs763877578", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763877578" } ], "glycoeffect": [], "start_pos": 1190, "end_pos": 1190, "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082204", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1190", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1225270143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225270143" }, { "id": "rs1225270143", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1225270143#frequency_tab" }, { "id": "rs1225270143", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225270143" } ], "glycoeffect": [], "start_pos": 1191, "end_pos": 1191, "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082201", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1191", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1225270143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225270143" }, { "id": "rs1225270143", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1225270143#frequency_tab" }, { "id": "rs1225270143", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225270143" } ], "glycoeffect": [], "start_pos": 1191, "end_pos": 1191, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082201", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1191", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779505272", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779505272" }, { "id": "rs1779505272", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779505272#frequency_tab" }, { "id": "rs1779505272", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779505272" } ], "glycoeffect": [], "start_pos": 1192, "end_pos": 1192, "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082198", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1192", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779505040", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779505040" }, { "id": "rs1779505040", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779505040#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1193, "end_pos": 1193, "sequence_org": "Y", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082195", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1193", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757977761", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757977761" }, { "id": "rs757977761", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757977761" }, { "id": "rs757977761", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757977761" } ], "glycoeffect": [], "start_pos": 1194, "end_pos": 1194, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082192", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1194", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs981886961", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs981886961" }, { "id": "rs981886961", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs981886961" } ], "glycoeffect": [], "start_pos": 1195, "end_pos": 1195, "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082189", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1195", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs752324242", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752324242" }, { "id": "rs752324242", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752324242" }, { "id": "rs752324242", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752324242" } ], "glycoeffect": [], "start_pos": 1195, "end_pos": 1195, "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082188", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1195", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs981886961", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs981886961" }, { "id": "rs981886961", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs981886961" } ], "glycoeffect": [], "start_pos": 1195, "end_pos": 1195, "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082189", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1195", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764681855", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764681855" }, { "id": "rs764681855", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764681855" }, { "id": "rs764681855", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764681855" } ], "glycoeffect": [], "start_pos": 1196, "end_pos": 1196, "sequence_org": "R", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082185", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1196", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779503596", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779503596" }, { "id": "rs1779503596", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779503596" } ], "glycoeffect": [], "start_pos": 1197, "end_pos": 1197, "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082182", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1197", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1325952919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1325952919" }, { "id": "rs1325952919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1325952919" } ], "glycoeffect": [], "start_pos": 1198, "end_pos": 1198, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082179", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1198", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1349800834", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349800834" }, { "id": "rs1349800834", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349800834#frequency_tab" }, { "id": "rs1349800834", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1349800834" }, { "id": "rs1349800834", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349800834" } ], "glycoeffect": [], "start_pos": 1199, "end_pos": 1199, "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "NC_000006.12", "chr_pos": "32082176", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "0.000010", "site_lbl": "R1199", "keywords": [ "ebi", "somatic", "germline" ] }, { "evidence": [ { "id": "rs1462486516", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1462486516" }, { "id": "rs1462486516", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1462486516" }, { "id": "rs1462486516", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1462486516" } ], "glycoeffect": [], "start_pos": 1199, "end_pos": 1199, "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082177", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1199", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 119, "end_pos": 119, "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097844", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E119", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1416828643", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1416828643" }, { "id": "rs1416828643", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1416828643#frequency_tab" }, { "id": "rs1416828643", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1416828643" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 11, "end_pos": 11, "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32098168", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S11", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1416828643", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1416828643" }, { "id": "rs1416828643", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1416828643#frequency_tab" }, { "id": "rs1416828643", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1416828643" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 11, "end_pos": 11, "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32098168", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S11", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779502101", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779502101" }, { "id": "rs1779502101", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779502101" } ], "glycoeffect": [], "start_pos": 1200, "end_pos": 1200, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082173", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1200", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779501865", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779501865" }, { "id": "rs1779501865", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779501865#frequency_tab" } ], "glycoeffect": [], "start_pos": 1201, "end_pos": 1201, "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082171", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1201", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1412461827", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1412461827" }, { "id": "rs1412461827", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1412461827#frequency_tab" }, { "id": "rs1412461827", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1412461827" } ], "glycoeffect": [], "start_pos": 1201, "end_pos": 1201, "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082169", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1201", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777320430", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777320430" }, { "id": "rs777320430", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777320430" }, { "id": "rs777320430", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777320430" }, { "id": "rs777320430", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs777320430" } ], "glycoeffect": [], "start_pos": 1202, "end_pos": 1202, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082168", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1202", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1582441805", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582441805" }, { "id": "rs1582441805", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1582441805" } ], "glycoeffect": [], "start_pos": 1203, "end_pos": 1203, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082165", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1203", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766971902", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766971902" }, { "id": "rs766971902", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766971902" }, { "id": "rs766971902", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766971902#frequency_tab" }, { "id": "rs766971902", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766971902" } ], "glycoeffect": [], "start_pos": 1205, "end_pos": 1205, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082159", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1205", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127256661", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127256661" }, { "id": "rs2127256661", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127256661" }, { "id": "rs2127256661", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2127256661" } ], "glycoeffect": [], "start_pos": 1207, "end_pos": 1207, "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082153", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1207", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1268252054", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1268252054" }, { "id": "rs1268252054", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1268252054#frequency_tab" }, { "id": "rs1268252054", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1268252054" } ], "glycoeffect": [], "start_pos": 1209, "end_pos": 1209, "sequence_org": "E", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082146", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1209", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772414777", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772414777" }, { "id": "rs772414777", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772414777" }, { "id": "rs772414777", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772414777#frequency_tab" }, { "id": "rs772414777", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772414777" } ], "glycoeffect": [], "start_pos": 1209, "end_pos": 1209, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082147", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1209", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772414777", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772414777" }, { "id": "rs772414777", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772414777" }, { "id": "rs772414777", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772414777#frequency_tab" }, { "id": "rs772414777", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772414777" } ], "glycoeffect": [], "start_pos": 1209, "end_pos": 1209, "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082147", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1209", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775116960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775116960" }, { "id": "rs775116960", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775116960" }, { "id": "rs775116960", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775116960" } ], "glycoeffect": [], "start_pos": 120, "end_pos": 120, "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097841", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q120", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748330632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748330632" }, { "id": "rs748330632", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748330632" }, { "id": "rs748330632", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748330632#frequency_tab" }, { "id": "rs748330632", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748330632" } ], "glycoeffect": [], "start_pos": 1210, "end_pos": 1210, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082144", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1210", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1194335452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194335452" }, { "id": "rs1194335452", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194335452#frequency_tab" }, { "id": "rs1194335452", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194335452" }, { "id": "rs1194335452", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1194335452" } ], "glycoeffect": [], "start_pos": 1210, "end_pos": 1210, "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082143", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1210", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1194335452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194335452" }, { "id": "rs1194335452", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194335452#frequency_tab" }, { "id": "rs1194335452", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194335452" } ], "glycoeffect": [], "start_pos": 1210, "end_pos": 1210, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082143", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1210", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748330632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748330632" }, { "id": "rs748330632", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748330632" }, { "id": "rs748330632", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748330632#frequency_tab" }, { "id": "rs748330632", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748330632" } ], "glycoeffect": [], "start_pos": 1210, "end_pos": 1210, "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082144", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1210", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1582441689", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582441689" }, { "id": "rs1582441689", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1582441689" } ], "glycoeffect": [], "start_pos": 1213, "end_pos": 1213, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082134", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1213", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774582576", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774582576" }, { "id": "rs774582576", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774582576" }, { "id": "rs774582576", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774582576#frequency_tab" }, { "id": "rs774582576", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774582576" } ], "glycoeffect": [], "start_pos": 1213, "end_pos": 1213, "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082135", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1213", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774582576", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774582576" }, { "id": "rs774582576", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774582576" }, { "id": "rs774582576", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774582576#frequency_tab" }, { "id": "rs774582576", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774582576" } ], "glycoeffect": [], "start_pos": 1213, "end_pos": 1213, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082135", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1213", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1244913427", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1244913427" }, { "id": "rs1244913427", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1244913427" } ], "glycoeffect": [], "start_pos": 1214, "end_pos": 1214, "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082132", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1214", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779497979", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779497979" }, { "id": "rs1779497979", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779497979#frequency_tab" }, { "id": "rs1779497979", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779497979" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1215, "end_pos": 1215, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082128", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1215", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779497711", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779497711" }, { "id": "rs1779497711", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779497711" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1216, "end_pos": 1216, "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082125", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1216", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779497460", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779497460" }, { "id": "rs1779497460", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779497460#frequency_tab" } ], "glycoeffect": [], "start_pos": 1217, "end_pos": 1217, "sequence_org": "L", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082123", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs138300355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138300355" }, { "id": "rs138300355", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138300355" }, { "id": "rs138300355", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138300355" }, { "id": "rs138300355", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138300355#frequency_tab" }, { "id": "rs138300355", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138300355" } ], "glycoeffect": [], "start_pos": 1218, "end_pos": 1218, "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082118", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00156986", "site_lbl": "D1218", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779497133", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779497133" }, { "id": "rs1779497133", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779497133#frequency_tab" } ], "glycoeffect": [], "start_pos": 1218, "end_pos": 1218, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082120", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1218", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749332638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749332638" }, { "id": "rs749332638", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749332638" }, { "id": "rs749332638", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749332638" } ], "glycoeffect": [], "start_pos": 1219, "end_pos": 1219, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082117", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1219", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757169367", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757169367" }, { "id": "rs757169367", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757169367" }, { "id": "rs757169367", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757169367#frequency_tab" }, { "id": "rs757169367", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757169367" } ], "glycoeffect": [], "start_pos": 1220, "end_pos": 1220, "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082113", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1220", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779496382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779496382" }, { "id": "rs1779496382", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779496382" } ], "glycoeffect": [], "start_pos": 1220, "end_pos": 1220, "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082114", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1220", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757169367", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757169367" }, { "id": "rs757169367", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757169367" }, { "id": "rs757169367", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757169367#frequency_tab" }, { "id": "rs757169367", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757169367" } ], "glycoeffect": [], "start_pos": 1220, "end_pos": 1220, "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082113", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1220", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746868657", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746868657" }, { "id": "rs746868657", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746868657" }, { "id": "rs746868657", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746868657" } ], "glycoeffect": [], "start_pos": 1221, "end_pos": 1221, "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082110", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1221", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746868657", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746868657" }, { "id": "rs746868657", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746868657" }, { "id": "rs746868657", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746868657" } ], "glycoeffect": [], "start_pos": 1221, "end_pos": 1221, "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082110", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1221", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199977034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199977034" }, { "id": "rs199977034", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199977034" }, { "id": "rs199977034", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199977034#frequency_tab" }, { "id": "rs199977034", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199977034" } ], "glycoeffect": [], "start_pos": 1222, "end_pos": 1222, "sequence_org": "K", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082107", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1222", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1303576995", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1303576995" }, { "id": "rs1303576995", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1303576995#frequency_tab" }, { "id": "rs1303576995", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1303576995" } ], "glycoeffect": [], "start_pos": 1224, "end_pos": 1224, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082102", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1224", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758166373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758166373" }, { "id": "rs758166373", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758166373" }, { "id": "rs758166373", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758166373" } ], "glycoeffect": [], "start_pos": 1225, "end_pos": 1225, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082097", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1225", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1364802258", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1364802258" }, { "id": "rs1364802258", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1364802258#frequency_tab" }, { "id": "rs1364802258", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1364802258" } ], "glycoeffect": [], "start_pos": 1227, "end_pos": 1227, "sequence_org": "L", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082093", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1227", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1292326989", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1292326989" }, { "id": "rs1292326989", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1292326989" } ], "glycoeffect": [], "start_pos": 1227, "end_pos": 1227, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082092", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1227", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1346211489", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1346211489" }, { "id": "rs1346211489", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1346211489" } ], "glycoeffect": [], "start_pos": 1228, "end_pos": 1228, "sequence_org": "F", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082089", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1228", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1158386100", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1158386100" }, { "id": "rs1158386100", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1158386100" } ], "glycoeffect": [], "start_pos": 1229, "end_pos": 1229, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082087", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1229", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1411732850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1411732850" }, { "id": "rs1411732850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1411732850#frequency_tab" }, { "id": "rs1411732850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1411732850" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 122, "end_pos": 122, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097835", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T122", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1411732850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1411732850" }, { "id": "rs1411732850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1411732850#frequency_tab" }, { "id": "rs1411732850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1411732850" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 122, "end_pos": 122, "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097835", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T122", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs752326127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752326127" }, { "id": "rs752326127", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752326127" }, { "id": "rs752326127", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752326127" } ], "glycoeffect": [], "start_pos": 1230, "end_pos": 1230, "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082083", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1230", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs146399029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146399029" }, { "id": "rs146399029", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146399029" }, { "id": "rs146399029", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146399029" }, { "id": "rs146399029", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146399029#frequency_tab" }, { "id": "rs146399029", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146399029" } ], "glycoeffect": [], "start_pos": 1231, "end_pos": 1231, "sequence_org": "A", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082080", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A1231", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs146399029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146399029" }, { "id": "rs146399029", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146399029" }, { "id": "rs146399029", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146399029" }, { "id": "rs146399029", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146399029#frequency_tab" }, { "id": "rs146399029", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146399029" } ], "glycoeffect": [], "start_pos": 1231, "end_pos": 1231, "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082080", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A1231", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs146399029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146399029" }, { "id": "rs146399029", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146399029" }, { "id": "rs146399029", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146399029" }, { "id": "rs146399029", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146399029#frequency_tab" }, { "id": "rs146399029", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146399029" }, { "id": "rs146399029", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146399029" } ], "glycoeffect": [], "start_pos": 1231, "end_pos": 1231, "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082080", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A1231", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs899663568", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs899663568" }, { "id": "rs899663568", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs899663568" } ], "glycoeffect": [], "start_pos": 1235, "end_pos": 1235, "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082068", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1235", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs754586168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754586168" }, { "id": "rs754586168", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754586168" }, { "id": "rs754586168", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754586168" }, { "id": "rs754586168", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754586168#frequency_tab" }, { "id": "rs754586168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754586168" } ], "glycoeffect": [], "start_pos": 1235, "end_pos": 1235, "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082069", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "R1235", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1216307507", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216307507" }, { "id": "rs1216307507", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1216307507#frequency_tab" }, { "id": "rs1216307507", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216307507" } ], "glycoeffect": [], "start_pos": 1237, "end_pos": 1237, "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082062", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1237", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1216307507", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216307507" }, { "id": "rs1216307507", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1216307507#frequency_tab" }, { "id": "rs1216307507", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216307507" } ], "glycoeffect": [], "start_pos": 1237, "end_pos": 1237, "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082062", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1237", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1486134966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1486134966" }, { "id": "rs1486134966", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1486134966#frequency_tab" }, { "id": "rs1486134966", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1486134966" } ], "glycoeffect": [], "start_pos": 1237, "end_pos": 1237, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082063", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1237", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1214157253", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1214157253" }, { "id": "rs1214157253", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1214157253" } ], "glycoeffect": [], "start_pos": 1238, "end_pos": 1238, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082059", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1238", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1262284533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262284533" }, { "id": "rs1262284533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262284533" } ], "glycoeffect": [], "start_pos": 1238, "end_pos": 1238, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082060", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1238", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1019829216", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1019829216" }, { "id": "rs1019829216", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1019829216#frequency_tab" }, { "id": "rs1019829216", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1019829216" } ], "glycoeffect": [], "start_pos": 1239, "end_pos": 1239, "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082057", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1239", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1397478440", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1397478440" }, { "id": "rs1397478440", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1397478440#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1240, "end_pos": 1240, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082054", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1240", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1280608503", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1280608503" }, { "id": "rs1280608503", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1280608503#frequency_tab" }, { "id": "rs1280608503", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1280608503" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1240, "end_pos": 1240, "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082053", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1240", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs576485554", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576485554" }, { "id": "rs576485554", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs576485554" }, { "id": "rs576485554", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs576485554" } ], "glycoeffect": [], "start_pos": 1241, "end_pos": 1241, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082050", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A1241", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773796746", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773796746" }, { "id": "rs773796746", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773796746" }, { "id": "rs773796746", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773796746#frequency_tab" }, { "id": "rs773796746", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773796746" } ], "glycoeffect": [], "start_pos": 1242, "end_pos": 1242, "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082048", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1242", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs558240500", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558240500" }, { "id": "rs558240500", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs558240500" }, { "id": "rs558240500", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558240500" }, { "id": "rs558240500", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs558240500#frequency_tab" }, { "id": "rs558240500", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558240500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1244, "end_pos": 1244, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082041", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T1244", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs558240500", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558240500" }, { "id": "rs558240500", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs558240500" }, { "id": "rs558240500", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558240500" }, { "id": "rs558240500", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs558240500#frequency_tab" }, { "id": "rs558240500", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558240500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1244, "end_pos": 1244, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082041", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T1244", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767794379", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767794379" }, { "id": "rs767794379", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767794379" }, { "id": "rs767794379", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767794379#frequency_tab" }, { "id": "rs767794379", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767794379" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1244, "end_pos": 1244, "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082042", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1244", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1377610482", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1377610482" }, { "id": "rs1377610482", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1377610482#frequency_tab" }, { "id": "rs1377610482", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1377610482" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1245, "end_pos": 1245, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082038", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1245", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1377610482", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1377610482" }, { "id": "rs1377610482", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1377610482#frequency_tab" }, { "id": "rs1377610482", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1377610482" } ], "glycoeffect": [], "start_pos": 1245, "end_pos": 1245, "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082038", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1245", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1303665712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1303665712" }, { "id": "rs1303665712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1303665712" } ], "glycoeffect": [], "start_pos": 1246, "end_pos": 1246, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32082036", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1246", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1329365278", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1329365278" }, { "id": "rs1329365278", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1329365278" } ], "glycoeffect": [], "start_pos": 1246, "end_pos": 1246, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081673", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1246", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753475458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753475458" }, { "id": "rs753475458", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753475458" }, { "id": "rs753475458", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs753475458" } ], "glycoeffect": [], "start_pos": 1248, "end_pos": 1248, "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081666", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1248", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1371252877", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1371252877" }, { "id": "rs1371252877", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1371252877" } ], "glycoeffect": [], "start_pos": 1248, "end_pos": 1248, "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081667", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1248", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1463010437", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463010437" }, { "id": "rs1463010437", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463010437" }, { "id": "rs1463010437", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1463010437" } ], "glycoeffect": [], "start_pos": 1248, "end_pos": 1248, "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081668", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1248", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs529991443", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529991443" }, { "id": "rs529991443", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs529991443" }, { "id": "rs529991443", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs529991443#frequency_tab" }, { "id": "rs529991443", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs529991443" } ], "glycoeffect": [], "start_pos": 1249, "end_pos": 1249, "sequence_org": "R", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081664", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R1249", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1780497714", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780497714" }, { "id": "rs1780497714", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1780497714#frequency_tab" } ], "glycoeffect": [], "start_pos": 124, "end_pos": 124, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097828", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G124", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1456225760", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456225760" }, { "id": "rs1456225760", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456225760" } ], "glycoeffect": [], "start_pos": 1250, "end_pos": 1250, "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081661", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1250", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1365273632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365273632" }, { "id": "rs1365273632", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1365273632" } ], "glycoeffect": [], "start_pos": 1251, "end_pos": 1251, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081659", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1251", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779724516", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779724516" }, { "id": "rs779724516", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779724516" }, { "id": "rs779724516", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779724516#frequency_tab" }, { "id": "rs779724516", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779724516" } ], "glycoeffect": [], "start_pos": 1252, "end_pos": 1252, "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081654", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1252", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1438661354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438661354" }, { "id": "rs1438661354", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438661354#frequency_tab" }, { "id": "rs1438661354", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438661354" } ], "glycoeffect": [], "start_pos": 1253, "end_pos": 1253, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081653", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1253", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs188789382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188789382" }, { "id": "rs188789382", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188789382" }, { "id": "rs188789382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188789382" }, { "id": "rs188789382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188789382#frequency_tab" }, { "id": "rs188789382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188789382" } ], "glycoeffect": [], "start_pos": 1253, "end_pos": 1253, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081652", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00137363", "site_lbl": "P1253", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs188789382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188789382" }, { "id": "rs188789382", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188789382" }, { "id": "rs188789382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188789382" }, { "id": "rs188789382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188789382#frequency_tab" }, { "id": "rs188789382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188789382" } ], "glycoeffect": [], "start_pos": 1253, "end_pos": 1253, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081652", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.00137363", "site_lbl": "P1253", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs188789382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188789382" }, { "id": "rs188789382", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188789382" }, { "id": "rs188789382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188789382" }, { "id": "rs188789382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188789382#frequency_tab" }, { "id": "rs188789382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188789382" } ], "glycoeffect": [], "start_pos": 1253, "end_pos": 1253, "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081652", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.00137363", "site_lbl": "P1253", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1438661354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438661354" }, { "id": "rs1438661354", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438661354#frequency_tab" }, { "id": "rs1438661354", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438661354" } ], "glycoeffect": [], "start_pos": 1253, "end_pos": 1253, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081653", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1253", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs762130701", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762130701" }, { "id": "rs762130701", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762130701" }, { "id": "rs762130701", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762130701#frequency_tab" }, { "id": "rs762130701", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762130701" } ], "glycoeffect": [], "start_pos": 1254, "end_pos": 1254, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081649", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1254", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs762130701", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762130701" }, { "id": "rs762130701", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762130701" }, { "id": "rs762130701", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762130701#frequency_tab" }, { "id": "rs762130701", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762130701" } ], "glycoeffect": [], "start_pos": 1254, "end_pos": 1254, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081649", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1254", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs762130701", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762130701" }, { "id": "rs762130701", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762130701" }, { "id": "rs762130701", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762130701#frequency_tab" }, { "id": "rs762130701", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762130701" } ], "glycoeffect": [], "start_pos": 1254, "end_pos": 1254, "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081649", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1254", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ] }, { "evidence": [ { "id": "rs1779453366", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779453366" }, { "id": "rs1779453366", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779453366#frequency_tab" } ], "glycoeffect": [], "start_pos": 1254, "end_pos": 1254, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081650", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1254", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376472382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376472382" }, { "id": "rs376472382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376472382" }, { "id": "rs376472382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376472382#frequency_tab" }, { "id": "rs376472382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376472382" }, { "id": "rs376472382", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs376472382" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081647", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1255", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs2127255245", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127255245" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081646_32081647delin", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1255", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376472382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376472382" }, { "id": "rs376472382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376472382" }, { "id": "rs376472382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376472382#frequency_tab" }, { "id": "rs376472382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376472382" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081647", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1255", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs12211410", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs12211410" }, { "id": "rs12211410", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs12211410" }, { "id": "rs12211410", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs12211410" }, { "id": "rs12211410", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs12211410#frequency_tab" }, { "id": "rs12211410", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs12211410" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081646", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.0985086", "site_lbl": "R1255", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs12211410", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs12211410" }, { "id": "rs12211410", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs12211410" }, { "id": "rs12211410", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs12211410" }, { "id": "rs12211410", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs12211410#frequency_tab" }, { "id": "rs12211410", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs12211410" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081646", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.0985086", "site_lbl": "R1255", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376472382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376472382" }, { "id": "rs376472382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376472382" }, { "id": "rs376472382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376472382#frequency_tab" }, { "id": "rs376472382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376472382" }, { "id": "rs376472382", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs376472382" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081647", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1255", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs2127255245", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127255245" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081646_32081647delin", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1255", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs765028734", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765028734" } ], "glycoeffect": [], "start_pos": 1255, "end_pos": 1255, "sequence_org": "R", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081653", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1255", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1262845873", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262845873" }, { "id": "rs1262845873", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262845873" } ], "glycoeffect": [], "start_pos": 1256, "end_pos": 1256, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081644", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1256", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779451007", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779451007" }, { "id": "rs1779451007", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779451007" } ], "glycoeffect": [], "start_pos": 1256, "end_pos": 1256, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081643", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1256", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1262845873", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262845873" }, { "id": "rs1262845873", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262845873" } ], "glycoeffect": [], "start_pos": 1256, "end_pos": 1256, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081644", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1256", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs908327210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs908327210" }, { "id": "rs908327210", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs908327210" } ], "glycoeffect": [], "start_pos": 1257, "end_pos": 1257, "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081639", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1257", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779450766", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779450766" }, { "id": "rs1779450766", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779450766" } ], "glycoeffect": [], "start_pos": 1257, "end_pos": 1257, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081641", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1257", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772034728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772034728" }, { "id": "rs772034728", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772034728" }, { "id": "rs772034728", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772034728#frequency_tab" }, { "id": "rs772034728", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772034728" } ], "glycoeffect": [], "start_pos": 1257, "end_pos": 1257, "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081640", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1257", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770463109", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770463109" }, { "id": "rs770463109", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770463109" }, { "id": "rs770463109", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770463109#frequency_tab" }, { "id": "rs770463109", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770463109" } ], "glycoeffect": [], "start_pos": 125, "end_pos": 125, "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097825", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C125", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1307248598", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1307248598" }, { "id": "rs1307248598", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1307248598#frequency_tab" }, { "id": "rs1307248598", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1307248598" } ], "glycoeffect": [], "start_pos": 1260, "end_pos": 1260, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081632", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1260", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747962258", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747962258" }, { "id": "rs747962258", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747962258" } ], "glycoeffect": [], "start_pos": 1262, "end_pos": 1262, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081625", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1262", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1418667724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1418667724" }, { "id": "rs1418667724", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1418667724#frequency_tab" }, { "id": "rs1418667724", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1418667724" } ], "glycoeffect": [], "start_pos": 1262, "end_pos": 1262, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081626", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1262", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779448306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779448306" }, { "id": "rs1779448306", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779448306" } ], "glycoeffect": [], "start_pos": 1263, "end_pos": 1263, "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081623", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1263", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1311184703", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1311184703" }, { "id": "rs1311184703", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1311184703#frequency_tab" } ], "glycoeffect": [], "start_pos": 1265, "end_pos": 1265, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081616", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1265", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779447100", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779447100" }, { "id": "rs1779447100", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779447100#frequency_tab" } ], "glycoeffect": [], "start_pos": 1266, "end_pos": 1266, "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081614", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1266", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1386918013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386918013" }, { "id": "rs1386918013", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386918013" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1270, "end_pos": 1270, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081601", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1270", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755723728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755723728" }, { "id": "rs755723728", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755723728" }, { "id": "rs755723728", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755723728#frequency_tab" }, { "id": "rs755723728", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755723728" } ], "glycoeffect": [], "start_pos": 1271, "end_pos": 1271, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081599", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1271", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749925578", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749925578" }, { "id": "rs749925578", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749925578" }, { "id": "rs749925578", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749925578#frequency_tab" }, { "id": "rs749925578", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749925578" }, { "id": "rs749925578", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs749925578" } ], "glycoeffect": [], "start_pos": 1272, "end_pos": 1272, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081596", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1272", "keywords": [ "ebi", "somatic", "disease" ], "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ] }, { "evidence": [ { "id": "rs1228236916", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1228236916" }, { "id": "rs1228236916", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1228236916#frequency_tab" }, { "id": "rs1228236916", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1228236916" } ], "glycoeffect": [], "start_pos": 1274, "end_pos": 1274, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081589", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1274", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1582439743", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1582439743" }, { "id": "rs1582439743", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1582439743" } ], "glycoeffect": [], "start_pos": 1274, "end_pos": 1274, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081590", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1274", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1376530498", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376530498" }, { "id": "rs1376530498", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376530498" } ], "glycoeffect": [], "start_pos": 1275, "end_pos": 1275, "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081585", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1275", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1342196320", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1342196320" }, { "id": "rs1342196320", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1342196320#frequency_tab" }, { "id": "rs1342196320", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1342196320" }, { "id": "rs1342196320", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1342196320" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1276, "end_pos": 1276, "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081583", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1276", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs879263799", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs879263799" }, { "id": "rs879263799", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs879263799#frequency_tab" }, { "id": "rs879263799", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs879263799" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1276, "end_pos": 1276, "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081584", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1276", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ] }, { "evidence": [ { "id": "rs370069053", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370069053" }, { "id": "rs370069053", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370069053" }, { "id": "rs370069053", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370069053#frequency_tab" }, { "id": "rs370069053", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370069053" }, { "id": "rs370069053", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs370069053" } ], "glycoeffect": [], "start_pos": 1278, "end_pos": 1278, "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081578", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1278", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs368042869", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368042869" }, { "id": "rs368042869", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs368042869" }, { "id": "rs368042869", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368042869" }, { "id": "rs368042869", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368042869#frequency_tab" }, { "id": "rs368042869", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368042869" }, { "id": "rs368042869", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs368042869" } ], "glycoeffect": [], "start_pos": 1278, "end_pos": 1278, "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081577", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1278", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs368042869", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368042869" }, { "id": "rs368042869", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs368042869" }, { "id": "rs368042869", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368042869" }, { "id": "rs368042869", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368042869#frequency_tab" }, { "id": "rs368042869", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368042869" } ], "glycoeffect": [], "start_pos": 1278, "end_pos": 1278, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081577", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1278", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs370069053", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370069053" }, { "id": "rs370069053", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370069053" }, { "id": "rs370069053", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370069053#frequency_tab" }, { "id": "rs370069053", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370069053" } ], "glycoeffect": [], "start_pos": 1278, "end_pos": 1278, "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081578", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1278", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1033737079", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033737079" }, { "id": "rs1033737079", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1033737079#frequency_tab" }, { "id": "rs1033737079", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1033737079" }, { "id": "rs1033737079", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1033737079" } ], "glycoeffect": [], "start_pos": 1279, "end_pos": 1279, "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081575", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1279", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1033737079", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033737079" }, { "id": "rs1033737079", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1033737079#frequency_tab" }, { "id": "rs1033737079", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1033737079" } ], "glycoeffect": [], "start_pos": 1279, "end_pos": 1279, "sequence_org": "L", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081575", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1279", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746370739", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746370739" }, { "id": "rs746370739", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746370739" }, { "id": "rs746370739", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746370739#frequency_tab" }, { "id": "rs746370739", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746370739" } ], "glycoeffect": [], "start_pos": 127, "end_pos": 127, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097820", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P127", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776915229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776915229" }, { "id": "rs776915229", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776915229" }, { "id": "rs776915229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776915229" } ], "glycoeffect": [], "start_pos": 127, "end_pos": 127, "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097819", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P127", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 127, "end_pos": 127, "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097820", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P127", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs752960555", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752960555" }, { "id": "rs752960555", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752960555" }, { "id": "rs752960555", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752960555" } ], "glycoeffect": [], "start_pos": 1281, "end_pos": 1281, "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081568", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W1281", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763267654", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763267654" }, { "id": "rs763267654", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763267654" }, { "id": "rs763267654", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763267654" } ], "glycoeffect": [], "start_pos": 1281, "end_pos": 1281, "sequence_org": "W", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081569", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W1281", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779440934", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779440934" } ], "glycoeffect": [], "start_pos": 1283, "end_pos": 1283, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081563", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1283", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779440934", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779440934" }, { "id": "rs1779440934", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779440934#frequency_tab" } ], "glycoeffect": [], "start_pos": 1283, "end_pos": 1283, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081563", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1283", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764901394", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764901394" }, { "id": "rs764901394", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764901394#frequency_tab" }, { "id": "rs764901394", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764901394" } ], "glycoeffect": [], "start_pos": 1285, "end_pos": 1285, "sequence_org": "Q", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081556", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1285", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs765426065", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765426065" }, { "id": "rs765426065", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765426065" }, { "id": "rs765426065", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765426065" } ], "glycoeffect": [], "start_pos": 1286, "end_pos": 1286, "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081553", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1286", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1231064005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1231064005" }, { "id": "rs1231064005", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1231064005#frequency_tab" }, { "id": "rs1231064005", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1231064005" } ], "glycoeffect": [], "start_pos": 1287, "end_pos": 1287, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081551", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1287", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1231064005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1231064005" }, { "id": "rs1231064005", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1231064005#frequency_tab" }, { "id": "rs1231064005", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1231064005" } ], "glycoeffect": [], "start_pos": 1287, "end_pos": 1287, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081551", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1287", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs574036721", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs574036721" }, { "id": "rs574036721", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs574036721" }, { "id": "rs574036721", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs574036721#frequency_tab" }, { "id": "rs574036721", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs574036721" } ], "glycoeffect": [], "start_pos": 1288, "end_pos": 1288, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081546", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1288", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1328111155", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328111155" }, { "id": "rs1328111155", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1328111155" } ], "glycoeffect": [], "start_pos": 1288, "end_pos": 1288, "sequence_org": "F", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081548", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1288", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1562879346", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1562879346" }, { "id": "rs1562879346", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1562879346" } ], "glycoeffect": [], "start_pos": 128, "end_pos": 128, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097816", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A128", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779438824", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779438824" }, { "id": "rs1779438824", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779438824#frequency_tab" }, { "id": "rs1779438824", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779438824" } ], "glycoeffect": [], "start_pos": 1291, "end_pos": 1291, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081537", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1291", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1358344515", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1358344515" }, { "id": "rs1358344515", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1358344515#frequency_tab" }, { "id": "rs1358344515", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1358344515" } ], "glycoeffect": [], "start_pos": 1292, "end_pos": 1292, "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081534", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1292", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779437527", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779437527" }, { "id": "rs1779437527", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779437527" } ], "glycoeffect": [], "start_pos": 1292, "end_pos": 1292, "sequence_org": "M", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081535", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1292", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776770497", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776770497" }, { "id": "rs776770497", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776770497" }, { "id": "rs776770497", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776770497#frequency_tab" }, { "id": "rs776770497", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776770497" } ], "glycoeffect": [], "start_pos": 1292, "end_pos": 1292, "sequence_org": "M", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081536", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1292", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776770497", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776770497" }, { "id": "rs776770497", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776770497" }, { "id": "rs776770497", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776770497#frequency_tab" }, { "id": "rs776770497", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776770497" } ], "glycoeffect": [], "start_pos": 1292, "end_pos": 1292, "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081536", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1292", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1414662938", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1414662938" }, { "id": "rs1414662938", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1414662938" } ], "glycoeffect": [], "start_pos": 1294, "end_pos": 1294, "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081529", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1294", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770850741", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770850741" }, { "id": "rs770850741", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770850741" }, { "id": "rs770850741", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770850741#frequency_tab" }, { "id": "rs770850741", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770850741" } ], "glycoeffect": [], "start_pos": 1296, "end_pos": 1296, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081524", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1296", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1477360342", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1477360342" }, { "id": "rs1477360342", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1477360342#frequency_tab" }, { "id": "rs1477360342", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1477360342" } ], "glycoeffect": [], "start_pos": 1297, "end_pos": 1297, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081521", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1297", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs964015109", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs964015109" }, { "id": "rs964015109", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs964015109" } ], "glycoeffect": [], "start_pos": 1299, "end_pos": 1299, "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081514", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1299", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 129, "end_pos": 129, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097813", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S129", "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": "rs1194946992", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194946992" }, { "id": "rs1194946992", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194946992" } ], "glycoeffect": [], "start_pos": 1301, "end_pos": 1301, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081509", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs912454032", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs912454032" }, { "id": "rs912454032", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs912454032" } ], "glycoeffect": [], "start_pos": 1301, "end_pos": 1301, "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081507", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs761823492", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761823492" }, { "id": "rs761823492", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761823492" }, { "id": "rs761823492", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761823492#frequency_tab" }, { "id": "rs761823492", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761823492" } ], "glycoeffect": [], "start_pos": 1302, "end_pos": 1302, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081505", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1302", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774381322", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774381322" }, { "id": "rs774381322", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774381322" }, { "id": "rs774381322", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774381322" } ], "glycoeffect": [], "start_pos": 1303, "end_pos": 1303, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081503", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1303", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1562851618", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1562851618" } ], "glycoeffect": [], "start_pos": 1303, "end_pos": 1303, "sequence_org": "Q", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081502", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1303", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1779433327", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779433327" }, { "id": "rs1779433327", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779433327" } ], "glycoeffect": [], "start_pos": 1304, "end_pos": 1304, "sequence_org": "A", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081499", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1304", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1212558739", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1212558739" }, { "id": "rs1212558739", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1212558739#frequency_tab" }, { "id": "rs1212558739", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1212558739" } ], "glycoeffect": [], "start_pos": 1304, "end_pos": 1304, "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081500", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1304", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1212558739", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1212558739" }, { "id": "rs1212558739", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1212558739#frequency_tab" }, { "id": "rs1212558739", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1212558739" } ], "glycoeffect": [], "start_pos": 1304, "end_pos": 1304, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081500", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1304", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1198812392", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1198812392" }, { "id": "rs1198812392", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1198812392" } ], "glycoeffect": [], "start_pos": 1306, "end_pos": 1306, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081493", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1306", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768602702", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768602702" }, { "id": "rs768602702", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768602702" }, { "id": "rs768602702", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768602702#frequency_tab" }, { "id": "rs768602702", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768602702" } ], "glycoeffect": [], "start_pos": 1306, "end_pos": 1306, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081494", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1306", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs370444721", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370444721" }, { "id": "rs370444721", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370444721#frequency_tab" }, { "id": "rs370444721", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370444721" } ], "glycoeffect": [], "start_pos": 1307, "end_pos": 1307, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081491", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1307", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749058728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749058728" }, { "id": "rs749058728", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749058728" }, { "id": "rs749058728", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749058728#frequency_tab" }, { "id": "rs749058728", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749058728" }, { "id": "rs749058728", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs749058728" } ], "glycoeffect": [], "start_pos": 1308, "end_pos": 1308, "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081487", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1308", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs769553878", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769553878" }, { "id": "rs769553878", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769553878" }, { "id": "rs769553878", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769553878#frequency_tab" }, { "id": "rs769553878", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769553878" } ], "glycoeffect": [], "start_pos": 1309, "end_pos": 1309, "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081484", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1309", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1339074585", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1339074585" }, { "id": "rs1339074585", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1339074585#frequency_tab" } ], "glycoeffect": [], "start_pos": 130, "end_pos": 130, "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097810", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A130", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771337502", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771337502" }, { "id": "rs771337502", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771337502" }, { "id": "rs771337502", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771337502" } ], "glycoeffect": [], "start_pos": 130, "end_pos": 130, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097811", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A130", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1339074585", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1339074585" }, { "id": "rs1339074585", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1339074585#frequency_tab" } ], "glycoeffect": [], "start_pos": 130, "end_pos": 130, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097810", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A130", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779430602", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779430602" }, { "id": "rs1779430602", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779430602#frequency_tab" }, { "id": "rs1779430602", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779430602" } ], "glycoeffect": [], "start_pos": 1310, "end_pos": 1310, "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081481", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1310", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779430825", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779430825" }, { "id": "rs1779430825", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779430825" } ], "glycoeffect": [], "start_pos": 1310, "end_pos": 1310, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081482", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1310", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1294871605", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294871605" }, { "id": "rs1294871605", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294871605" } ], "glycoeffect": [], "start_pos": 1311, "end_pos": 1311, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081479", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1311", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1294871605", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294871605" } ], "glycoeffect": [], "start_pos": 1311, "end_pos": 1311, "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081479", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1311", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs780754411", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780754411" }, { "id": "rs780754411", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780754411" }, { "id": "rs780754411", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780754411#frequency_tab" }, { "id": "rs780754411", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780754411" } ], "glycoeffect": [], "start_pos": 1314, "end_pos": 1314, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081469", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1314", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs557311390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557311390" }, { "id": "rs557311390", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557311390" }, { "id": "rs557311390", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557311390" }, { "id": "rs557311390", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557311390#frequency_tab" }, { "id": "rs557311390", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557311390" } ], "glycoeffect": [], "start_pos": 1314, "end_pos": 1314, "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081470", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "V1314", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127254498", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127254498" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1315, "end_pos": 1315, "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081469", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1315", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ] }, { "evidence": [ { "id": "rs1400345607", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1400345607" }, { "id": "rs1400345607", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1400345607" } ], "glycoeffect": [], "start_pos": 1316, "end_pos": 1316, "sequence_org": "V", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081463", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1316", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127254476", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127254476" }, { "id": "rs2127254476", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127254476" } ], "glycoeffect": [], "start_pos": 1316, "end_pos": 1316, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081464", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1316", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778225501", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778225501" }, { "id": "rs778225501", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778225501" }, { "id": "rs778225501", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778225501#frequency_tab" }, { "id": "rs778225501", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778225501" } ], "glycoeffect": [], "start_pos": 1317, "end_pos": 1317, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081461", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1317", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs536142838", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536142838" }, { "id": "rs536142838", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536142838" }, { "id": "rs536142838", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536142838" }, { "id": "rs536142838", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs536142838#frequency_tab" }, { "id": "rs536142838", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs536142838" } ], "glycoeffect": [], "start_pos": 1318, "end_pos": 1318, "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081458", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "G1318", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs536142838", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536142838" }, { "id": "rs536142838", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536142838" }, { "id": "rs536142838", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536142838" }, { "id": "rs536142838", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs536142838#frequency_tab" }, { "id": "rs536142838", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs536142838" } ], "glycoeffect": [], "start_pos": 1318, "end_pos": 1318, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081458", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "G1318", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs536142838", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536142838" }, { "id": "rs536142838", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536142838" }, { "id": "rs536142838", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536142838" }, { "id": "rs536142838", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs536142838#frequency_tab" }, { "id": "rs536142838", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs536142838" } ], "glycoeffect": [], "start_pos": 1318, "end_pos": 1318, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081458", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "G1318", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1237120601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237120601" }, { "id": "rs1237120601", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237120601" } ], "glycoeffect": [], "start_pos": 1319, "end_pos": 1319, "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081455", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1319", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1320, "end_pos": 1320, "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "D", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32081451", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "D1320", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1779425833", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779425833" }, { "id": "rs1779425833", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779425833" } ], "glycoeffect": [], "start_pos": 1321, "end_pos": 1321, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081449", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1321", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1197983727", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1197983727" }, { "id": "rs1197983727", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1197983727" } ], "glycoeffect": [], "start_pos": 1322, "end_pos": 1322, "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081444", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1322", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1258771989", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258771989" }, { "id": "rs1258771989", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258771989" } ], "glycoeffect": [], "start_pos": 1322, "end_pos": 1322, "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081445", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1322", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1280340355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1280340355" }, { "id": "rs1280340355", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1280340355#frequency_tab" }, { "id": "rs1280340355", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1280340355" }, { "id": "rs1280340355", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1280340355" } ], "glycoeffect": [], "start_pos": 1322, "end_pos": 1322, "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081446", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1322", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs568613138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568613138" }, { "id": "rs568613138", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs568613138" }, { "id": "rs568613138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568613138" }, { "id": "rs568613138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs568613138#frequency_tab" }, { "id": "rs568613138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs568613138" } ], "glycoeffect": [], "start_pos": 1323, "end_pos": 1323, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081443", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R1323", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766503904", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766503904" }, { "id": "rs766503904", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766503904" }, { "id": "rs766503904", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766503904#frequency_tab" }, { "id": "rs766503904", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766503904" } ], "glycoeffect": [], "start_pos": 1323, "end_pos": 1323, "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081442", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1323", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs568613138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568613138" }, { "id": "rs568613138", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs568613138" }, { "id": "rs568613138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568613138" }, { "id": "rs568613138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs568613138#frequency_tab" }, { "id": "rs568613138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs568613138" } ], "glycoeffect": [], "start_pos": 1323, "end_pos": 1323, "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081443", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R1323", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs117635810", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117635810" } ], "glycoeffect": [], "start_pos": 1324, "end_pos": 1324, "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081438", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1324", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs55800491", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs55800491" }, { "id": "rs55800491", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs55800491" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1325, "end_pos": 1325, "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081437", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1325", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774469183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774469183" }, { "id": "rs774469183", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774469183" }, { "id": "rs774469183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774469183" } ], "glycoeffect": [], "start_pos": 1326, "end_pos": 1326, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081434", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1326", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764099103", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764099103" }, { "id": "rs764099103", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764099103" }, { "id": "rs764099103", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764099103#frequency_tab" }, { "id": "rs764099103", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764099103" } ], "glycoeffect": [], "start_pos": 1327, "end_pos": 1327, "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081429", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1327", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1443865278", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443865278" } ], "glycoeffect": [], "start_pos": 1328, "end_pos": 1328, "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081426", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1328", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1377043678", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1377043678" }, { "id": "rs1377043678", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1377043678" } ], "glycoeffect": [], "start_pos": 1329, "end_pos": 1329, "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081425", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1329", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1193091663", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1193091663" }, { "id": "rs1193091663", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1193091663#frequency_tab" } ], "glycoeffect": [], "start_pos": 1329, "end_pos": 1329, "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081424", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1329", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747265735", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747265735" }, { "id": "rs747265735", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747265735" }, { "id": "rs747265735", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747265735" } ], "glycoeffect": [], "start_pos": 132, "end_pos": 132, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097805", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A132", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1363532755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363532755" }, { "id": "rs1363532755", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1363532755" } ], "glycoeffect": [], "start_pos": 132, "end_pos": 132, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097804", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A132", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1406024505", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1406024505" }, { "id": "rs1406024505", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1406024505#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1330, "end_pos": 1330, "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081422", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1330", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs587777684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs587777684" }, { "id": "rs587777684", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs587777684" }, { "id": "23620400", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23620400" } ], "glycoeffect": [], "start_pos": 1331, "end_pos": 1331, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081419", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1331", "disease": [ { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs775418163", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775418163" }, { "id": "rs775418163", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775418163" }, { "id": "rs775418163", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775418163" }, { "id": "rs775418163", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs775418163" } ], "glycoeffect": [], "start_pos": 1333, "end_pos": 1333, "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081413", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1333", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs534979105", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534979105" }, { "id": "rs534979105", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534979105" }, { "id": "rs534979105", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534979105" }, { "id": "rs534979105", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534979105" } ], "glycoeffect": [], "start_pos": 1333, "end_pos": 1333, "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081412", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1333", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1413459862", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413459862" }, { "id": "rs1413459862", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413459862#frequency_tab" }, { "id": "rs1413459862", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413459862" } ], "glycoeffect": [], "start_pos": 1334, "end_pos": 1334, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081410", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1334", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1413459862", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413459862" }, { "id": "rs1413459862", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413459862#frequency_tab" }, { "id": "rs1413459862", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413459862" } ], "glycoeffect": [], "start_pos": 1334, "end_pos": 1334, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081410", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1334", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376857127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376857127" }, { "id": "rs376857127", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376857127#frequency_tab" }, { "id": "rs376857127", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376857127" } ], "glycoeffect": [], "start_pos": 1335, "end_pos": 1335, "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081405", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1335", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs570879376", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs570879376" }, { "id": "rs570879376", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs570879376" }, { "id": "rs570879376", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs570879376" } ], "glycoeffect": [], "start_pos": 1336, "end_pos": 1336, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081404", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "Q1336", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs745543647", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745543647" }, { "id": "rs745543647", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745543647" }, { "id": "rs745543647", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745543647#frequency_tab" }, { "id": "rs745543647", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745543647" } ], "glycoeffect": [], "start_pos": 1337, "end_pos": 1337, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081401", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1337", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs61735731", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735731" }, { "id": "rs61735731", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735731" }, { "id": "rs61735731", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735731" }, { "id": "rs61735731", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735731#frequency_tab" }, { "id": "rs61735731", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735731" } ], "glycoeffect": [], "start_pos": 1337, "end_pos": 1337, "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081400", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "R1337", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ] }, { "evidence": [ { "id": "rs61735731", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735731" }, { "id": "rs61735731", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735731" }, { "id": "rs61735731", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735731" }, { "id": "rs61735731", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735731#frequency_tab" }, { "id": "rs61735731", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735731" } ], "glycoeffect": [], "start_pos": 1337, "end_pos": 1337, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081400", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "R1337", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs61735731", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735731" }, { "id": "rs61735731", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735731" }, { "id": "rs61735731", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735731" }, { "id": "rs61735731", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735731#frequency_tab" }, { "id": "rs61735731", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735731" } ], "glycoeffect": [], "start_pos": 1337, "end_pos": 1337, "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081400", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "R1337", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774172352", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774172352" }, { "id": "rs774172352", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774172352#frequency_tab" }, { "id": "rs774172352", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774172352" } ], "glycoeffect": [], "start_pos": 1338, "end_pos": 1338, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081397", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1338", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746482679", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746482679" }, { "id": "rs746482679", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746482679" }, { "id": "rs746482679", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746482679#frequency_tab" }, { "id": "rs746482679", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746482679" } ], "glycoeffect": [], "start_pos": 1339, "end_pos": 1339, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081394", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1339", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1320915966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1320915966" }, { "id": "rs1320915966", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1320915966" } ], "glycoeffect": [], "start_pos": 1340, "end_pos": 1340, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081392", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1340", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs924349760", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs924349760" }, { "id": "rs924349760", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs924349760#frequency_tab" }, { "id": "rs924349760", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs924349760" } ], "glycoeffect": [], "start_pos": 1341, "end_pos": 1341, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081389", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1341", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779416950", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779416950" }, { "id": "rs1779416950", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779416950#frequency_tab" }, { "id": "rs1779416950", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779416950" } ], "glycoeffect": [], "start_pos": 1341, "end_pos": 1341, "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081388", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1341", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779416529", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779416529" }, { "id": "rs1779416529", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779416529" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1342, "end_pos": 1342, "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081386", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1342", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483668406", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483668406" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1342, "end_pos": 1342, "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081385", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1342", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1295822418", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1295822418" }, { "id": "rs1295822418", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1295822418" } ], "glycoeffect": [], "start_pos": 1345, "end_pos": 1345, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081377", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1345", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748589387", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748589387" }, { "id": "rs748589387", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748589387" }, { "id": "rs748589387", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748589387" } ], "glycoeffect": [], "start_pos": 1345, "end_pos": 1345, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081376", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1345", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127254038", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127254038" }, { "id": "rs2127254038", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127254038" } ], "glycoeffect": [], "start_pos": 1346, "end_pos": 1346, "sequence_org": "K", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081373", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1346", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1349706546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349706546" }, { "id": "rs1349706546", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349706546" } ], "glycoeffect": [], "start_pos": 1348, "end_pos": 1348, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32081368", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1348", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770478856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770478856" }, { "id": "rs770478856", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770478856" }, { "id": "rs770478856", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770478856" } ], "glycoeffect": [], "start_pos": 1349, "end_pos": 1349, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079362", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1349", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776399008", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776399008" }, { "id": "rs776399008", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776399008" }, { "id": "rs776399008", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776399008" } ], "glycoeffect": [], "start_pos": 1349, "end_pos": 1349, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079363", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1349", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2078174121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078174121" }, { "id": "rs2078174121", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2078174121#frequency_tab" } ], "glycoeffect": [], "start_pos": 1350, "end_pos": 1350, "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079359", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1350", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779308123", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779308123" }, { "id": "rs1779308123", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779308123#frequency_tab" } ], "glycoeffect": [], "start_pos": 1351, "end_pos": 1351, "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079356", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1351", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746592378", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746592378" }, { "id": "rs746592378", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746592378" }, { "id": "rs746592378", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746592378#frequency_tab" }, { "id": "rs746592378", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746592378" } ], "glycoeffect": [], "start_pos": 1354, "end_pos": 1354, "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079347", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1354", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs549679621", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549679621" }, { "id": "rs549679621", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549679621" }, { "id": "rs549679621", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549679621" }, { "id": "rs549679621", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549679621#frequency_tab" }, { "id": "rs549679621", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549679621" }, { "id": "rs549679621", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549679621" } ], "glycoeffect": [], "start_pos": 1355, "end_pos": 1355, "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079345", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1355", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779306868", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779306868" }, { "id": "rs1779306868", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779306868" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1356, "end_pos": 1356, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079341", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1356", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779306642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779306642" }, { "id": "rs1779306642", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779306642#frequency_tab" } ], "glycoeffect": [], "start_pos": 1357, "end_pos": 1357, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079339", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1357", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771514610", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771514610" }, { "id": "rs771514610", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771514610" }, { "id": "rs771514610", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771514610" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1358, "end_pos": 1358, "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079335", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1358", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs987430972", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs987430972" }, { "id": "rs987430972", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs987430972#frequency_tab" }, { "id": "rs987430972", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs987430972" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1358, "end_pos": 1358, "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079334", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1358", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748677323", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748677323" }, { "id": "rs748677323", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748677323" }, { "id": "rs748677323", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748677323" } ], "glycoeffect": [], "start_pos": 1359, "end_pos": 1359, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079333", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1359", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779248696", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779248696" }, { "id": "rs779248696", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779248696" }, { "id": "rs779248696", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779248696" } ], "glycoeffect": [], "start_pos": 1362, "end_pos": 1362, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079323", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1362", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750603754", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750603754" }, { "id": "rs750603754", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750603754" }, { "id": "rs750603754", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750603754#frequency_tab" }, { "id": "rs750603754", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750603754" } ], "glycoeffect": [], "start_pos": 1365, "end_pos": 1365, "sequence_org": "E", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079314", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1365", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1466044693", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1466044693" }, { "id": "rs1466044693", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1466044693" } ], "glycoeffect": [], "start_pos": 1366, "end_pos": 1366, "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079312", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1366", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs752709537", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752709537" }, { "id": "rs752709537", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752709537" }, { "id": "rs752709537", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752709537#frequency_tab" }, { "id": "rs752709537", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752709537" } ], "glycoeffect": [], "start_pos": 1367, "end_pos": 1367, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079308", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1367", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs752709537", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752709537" }, { "id": "rs752709537", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752709537" }, { "id": "rs752709537", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752709537#frequency_tab" }, { "id": "rs752709537", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752709537" } ], "glycoeffect": [], "start_pos": 1367, "end_pos": 1367, "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079308", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1367", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759438362", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759438362" }, { "id": "rs759438362", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759438362" }, { "id": "rs759438362", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759438362" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1369, "end_pos": 1369, "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079303", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1369", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs913492853", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs913492853" }, { "id": "rs913492853", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs913492853" }, { "id": "rs913492853", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs913492853#frequency_tab" }, { "id": "rs913492853", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs913492853" }, { "id": "rs913492853", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs913492853" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1369, "end_pos": 1369, "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079302", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1369", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1445017304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1445017304" }, { "id": "rs1445017304", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1445017304" } ], "glycoeffect": [], "start_pos": 136, "end_pos": 136, "sequence_org": "Q", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097447", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483767587", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483767587" } ], "glycoeffect": [], "start_pos": 136, "end_pos": 136, "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097446", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760334908", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760334908" }, { "id": "rs760334908", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760334908" }, { "id": "rs760334908", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760334908#frequency_tab" }, { "id": "rs760334908", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760334908" } ], "glycoeffect": [], "start_pos": 1371, "end_pos": 1371, "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079297", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1371", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760334908", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760334908" }, { "id": "rs760334908", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760334908" }, { "id": "rs760334908", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760334908#frequency_tab" }, { "id": "rs760334908", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760334908" }, { "id": "rs760334908", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760334908" } ], "glycoeffect": [], "start_pos": 1371, "end_pos": 1371, "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079297", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1371", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs771602314", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771602314" }, { "id": "rs771602314", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771602314" }, { "id": "rs771602314", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771602314#frequency_tab" }, { "id": "rs771602314", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771602314" } ], "glycoeffect": [], "start_pos": 1373, "end_pos": 1373, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079290", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1373", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs527420736", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527420736" }, { "id": "rs527420736", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs527420736" }, { "id": "rs527420736", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527420736" }, { "id": "rs527420736", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs527420736#frequency_tab" }, { "id": "rs527420736", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs527420736" } ], "glycoeffect": [], "start_pos": 1373, "end_pos": 1373, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079291", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "P1373", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1034520502", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1034520502" }, { "id": "rs1034520502", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1034520502#frequency_tab" }, { "id": "rs1034520502", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1034520502" } ], "glycoeffect": [], "start_pos": 1374, "end_pos": 1374, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079287", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1374", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127293541", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127293541" }, { "id": "rs2127293541", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127293541" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 137, "end_pos": 137, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097443", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T137", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779298897", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779298897" }, { "id": "rs1779298897", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779298897#frequency_tab" }, { "id": "rs1779298897", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779298897" } ], "glycoeffect": [], "start_pos": 1382, "end_pos": 1382, "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079264", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1382", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779298405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779298405" }, { "id": "rs1779298405", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779298405" }, { "id": "rs1779298405", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779298405" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1384, "end_pos": 1384, "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079257", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1384", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs780283718", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780283718" }, { "id": "rs780283718", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780283718" }, { "id": "rs780283718", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780283718#frequency_tab" }, { "id": "rs780283718", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780283718" } ], "glycoeffect": [], "start_pos": 1385, "end_pos": 1385, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079255", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1385", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779297660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779297660" }, { "id": "rs1779297660", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779297660#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1387, "end_pos": 1387, "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079249", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1387", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1170412765", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170412765" }, { "id": "rs1170412765", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170412765" } ], "glycoeffect": [], "start_pos": 138, "end_pos": 138, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097441", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D138", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781521699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781521699" }, { "id": "rs781521699", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781521699" }, { "id": "rs781521699", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781521699" } ], "glycoeffect": [], "start_pos": 1390, "end_pos": 1390, "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079240", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1390", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781521699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781521699" }, { "id": "rs781521699", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781521699" }, { "id": "rs781521699", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781521699" } ], "glycoeffect": [], "start_pos": 1390, "end_pos": 1390, "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079240", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1390", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2483654739", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483654739" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1393, "end_pos": 1393, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079231", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1393", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs541600049", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs541600049" }, { "id": "rs541600049", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs541600049" }, { "id": "rs541600049", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs541600049" }, { "id": "rs541600049", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs541600049#frequency_tab" }, { "id": "rs541600049", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs541600049" } ], "glycoeffect": [], "start_pos": 1394, "end_pos": 1394, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079228", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "V1394", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1281889688", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1281889688" }, { "id": "rs1281889688", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1281889688" }, { "id": "rs1281889688", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1281889688" } ], "glycoeffect": [], "start_pos": 1395, "end_pos": 1395, "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079224", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1395", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1421660297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421660297" }, { "id": "rs1421660297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1421660297" } ], "glycoeffect": [], "start_pos": 1395, "end_pos": 1395, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079225", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1395", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1421660297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421660297" }, { "id": "rs1421660297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1421660297" } ], "glycoeffect": [], "start_pos": 1395, "end_pos": 1395, "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079225", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1395", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1239538067", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1239538067" }, { "id": "rs1239538067", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1239538067#frequency_tab" }, { "id": "rs1239538067", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1239538067" }, { "id": "rs1239538067", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1239538067" } ], "glycoeffect": [], "start_pos": 1396, "end_pos": 1396, "sequence_org": "Q", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079221", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1396", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779295390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779295390" }, { "id": "rs1779295390", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779295390#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1398, "end_pos": 1398, "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079216", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1398", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775204788", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775204788" }, { "id": "rs775204788", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775204788" }, { "id": "rs775204788", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775204788" } ], "glycoeffect": [], "start_pos": 139, "end_pos": 139, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097438", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V139", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs898029071", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs898029071" }, { "id": "rs898029071", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs898029071" } ], "glycoeffect": [], "start_pos": 13, "end_pos": 13, "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32098162", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V13", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs898029071", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs898029071" }, { "id": "rs898029071", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs898029071" } ], "glycoeffect": [], "start_pos": 13, "end_pos": 13, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32098162", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V13", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1456879875", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456879875" }, { "id": "rs1456879875", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456879875#frequency_tab" }, { "id": "rs1456879875", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456879875" } ], "glycoeffect": [], "start_pos": 1400, "end_pos": 1400, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079210", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1400", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1372051078", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1372051078" }, { "id": "rs1372051078", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1372051078" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1401, "end_pos": 1401, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079206", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1401", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1194532133", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194532133" }, { "id": "rs1194532133", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194532133" } ], "glycoeffect": [], "start_pos": 1402, "end_pos": 1402, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079202", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1402", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766110850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766110850" }, { "id": "rs766110850", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766110850" }, { "id": "rs766110850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766110850#frequency_tab" }, { "id": "rs766110850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766110850" } ], "glycoeffect": [], "start_pos": 1404, "end_pos": 1404, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079198", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1404", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766110850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766110850" }, { "id": "rs766110850", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766110850" }, { "id": "rs766110850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766110850#frequency_tab" }, { "id": "rs766110850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766110850" }, { "id": "rs766110850", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs766110850" } ], "glycoeffect": [], "start_pos": 1404, "end_pos": 1404, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079198", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1404", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779292513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779292513" }, { "id": "rs1779292513", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779292513#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1406, "end_pos": 1406, "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079191", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1406", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760422687", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760422687" }, { "id": "rs760422687", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760422687" }, { "id": "rs760422687", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760422687" } ], "glycoeffect": [], "start_pos": 1407, "end_pos": 1407, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079189", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1407", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483654259", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483654259" } ], "glycoeffect": [], "start_pos": 1407, "end_pos": 1407, "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079188", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1407", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2127248947", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127248947" }, { "id": "rs2127248947", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127248947" } ], "glycoeffect": [], "start_pos": 1408, "end_pos": 1408, "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079186", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1408", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750116856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750116856" }, { "id": "rs750116856", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750116856" }, { "id": "rs750116856", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750116856" } ], "glycoeffect": [], "start_pos": 1409, "end_pos": 1409, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079183", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1409", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758876550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758876550" }, { "id": "rs758876550", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758876550" }, { "id": "rs758876550", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758876550#frequency_tab" }, { "id": "rs758876550", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758876550" } ], "glycoeffect": [], "start_pos": 140, "end_pos": 140, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097434", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R140", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758876550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758876550" }, { "id": "rs758876550", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758876550" }, { "id": "rs758876550", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758876550#frequency_tab" }, { "id": "rs758876550", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758876550" } ], "glycoeffect": [], "start_pos": 140, "end_pos": 140, "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097434", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R140", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758876550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758876550" }, { "id": "rs758876550", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758876550" }, { "id": "rs758876550", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758876550#frequency_tab" }, { "id": "rs758876550", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758876550" } ], "glycoeffect": [], "start_pos": 140, "end_pos": 140, "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097434", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R140", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs1420372911", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1420372911" }, { "id": "rs1420372911", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1420372911#frequency_tab" }, { "id": "rs1420372911", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1420372911" } ], "glycoeffect": [], "start_pos": 140, "end_pos": 140, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097435", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R140", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779291881", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779291881" }, { "id": "rs1779291881", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779291881" }, { "id": "rs1779291881", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779291881" } ], "glycoeffect": [], "start_pos": 1410, "end_pos": 1410, "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079180", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1410", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1321697677", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1321697677" }, { "id": "rs1321697677", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1321697677#frequency_tab" } ], "glycoeffect": [], "start_pos": 1411, "end_pos": 1411, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079177", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1411", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773727721", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773727721" }, { "id": "rs773727721", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773727721" }, { "id": "rs773727721", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773727721#frequency_tab" }, { "id": "rs773727721", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773727721" } ], "glycoeffect": [], "start_pos": 1412, "end_pos": 1412, "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079173", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1412", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs761371066", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761371066" }, { "id": "rs761371066", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761371066" }, { "id": "rs761371066", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761371066#frequency_tab" }, { "id": "rs761371066", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761371066" }, { "id": "rs761371066", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761371066" } ], "glycoeffect": [], "start_pos": 1412, "end_pos": 1412, "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079174", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1412", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779290580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779290580" }, { "id": "rs1779290580", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779290580#frequency_tab" } ], "glycoeffect": [], "start_pos": 1413, "end_pos": 1413, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079171", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1413", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483654069", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483654069" } ], "glycoeffect": [], "start_pos": 1413, "end_pos": 1413, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079170", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1413", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779290580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779290580" } ], "glycoeffect": [], "start_pos": 1413, "end_pos": 1413, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079171", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1413", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs565552445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565552445" }, { "id": "rs565552445", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs565552445" }, { "id": "rs565552445", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565552445" }, { "id": "rs565552445", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs565552445#frequency_tab" }, { "id": "rs565552445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs565552445" } ], "glycoeffect": [], "start_pos": 1414, "end_pos": 1414, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079168", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1414", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs9267799", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9267799" }, { "id": "rs9267799", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs9267799" }, { "id": "rs9267799", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9267799" }, { "id": "rs9267799", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs9267799#frequency_tab" }, { "id": "rs9267799", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs9267799" } ], "glycoeffect": [], "start_pos": 1414, "end_pos": 1414, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079167", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.0449372", "site_lbl": "R1414", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs9267799", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9267799" }, { "id": "rs9267799", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs9267799" }, { "id": "rs9267799", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9267799" }, { "id": "rs9267799", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs9267799#frequency_tab" }, { "id": "rs9267799", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs9267799" } ], "glycoeffect": [], "start_pos": 1414, "end_pos": 1414, "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079167", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.0449372", "site_lbl": "R1414", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs565552445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565552445" }, { "id": "rs565552445", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs565552445" }, { "id": "rs565552445", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565552445" }, { "id": "rs565552445", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs565552445#frequency_tab" }, { "id": "rs565552445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs565552445" }, { "id": "rs565552445", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs565552445" } ], "glycoeffect": [], "start_pos": 1414, "end_pos": 1414, "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079168", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1414", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs900415940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs900415940" }, { "id": "rs900415940", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs900415940#frequency_tab" }, { "id": "rs900415940", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs900415940" } ], "glycoeffect": [], "start_pos": 1415, "end_pos": 1415, "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079165", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1415", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs900415940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs900415940" }, { "id": "rs900415940", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs900415940#frequency_tab" }, { "id": "rs900415940", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs900415940" } ], "glycoeffect": [], "start_pos": 1415, "end_pos": 1415, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079165", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1415", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770309992", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770309992" }, { "id": "rs770309992", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770309992" }, { "id": "rs770309992", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770309992#frequency_tab" }, { "id": "rs770309992", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770309992" }, { "id": "rs770309992", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs770309992" } ], "glycoeffect": [], "start_pos": 1415, "end_pos": 1415, "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079164", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1415", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs943572831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs943572831" }, { "id": "rs943572831", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs943572831#frequency_tab" }, { "id": "rs943572831", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs943572831" }, { "id": "rs943572831", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs943572831" } ], "glycoeffect": [], "start_pos": 1417, "end_pos": 1417, "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079159", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1417", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs777054871", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777054871" }, { "id": "rs777054871", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777054871" }, { "id": "rs777054871", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777054871#frequency_tab" }, { "id": "rs777054871", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777054871" }, { "id": "rs777054871", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs777054871" } ], "glycoeffect": [], "start_pos": 1417, "end_pos": 1417, "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079158", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1417", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1043137957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1043137957" }, { "id": "rs1043137957", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1043137957#frequency_tab" }, { "id": "rs1043137957", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1043137957" } ], "glycoeffect": [], "start_pos": 1418, "end_pos": 1418, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079155", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1418", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771278790", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771278790" }, { "id": "rs771278790", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771278790" }, { "id": "rs771278790", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771278790" } ], "glycoeffect": [], "start_pos": 1419, "end_pos": 1419, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079152", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1419", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1780477817", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780477817" }, { "id": "rs1780477817", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1780477817#frequency_tab" }, { "id": "rs1780477817", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1780477817" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 141, "end_pos": 141, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097432", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T141", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1435420982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435420982" }, { "id": "rs1435420982", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435420982" } ], "glycoeffect": [], "start_pos": 1420, "end_pos": 1420, "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079150", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1420", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779287558", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779287558" }, { "id": "rs1779287558", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779287558" }, { "id": "rs1779287558", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779287558" } ], "glycoeffect": [], "start_pos": 1420, "end_pos": 1420, "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079149", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1420", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs6920695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs6920695" }, { "id": "rs6920695", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs6920695" } ], "glycoeffect": [], "start_pos": 1421, "end_pos": 1421, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079147", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1421", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs6920695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs6920695" }, { "id": "rs6920695", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs6920695" } ], "glycoeffect": [], "start_pos": 1421, "end_pos": 1421, "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079147", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1421", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779287112", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779287112" }, { "id": "rs1779287112", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779287112#frequency_tab" } ], "glycoeffect": [], "start_pos": 1421, "end_pos": 1421, "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079146", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1421", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1184281001", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1184281001" }, { "id": "rs1184281001", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1184281001#frequency_tab" } ], "glycoeffect": [], "start_pos": 1422, "end_pos": 1422, "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079142", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1422", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747190024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747190024" }, { "id": "rs747190024", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747190024" }, { "id": "rs747190024", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747190024#frequency_tab" } ], "glycoeffect": [], "start_pos": 1424, "end_pos": 1424, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079138", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1424", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779285537", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779285537" }, { "id": "rs1779285537", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779285537" }, { "id": "rs1779285537", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779285537#frequency_tab" } ], "glycoeffect": [], "start_pos": 1425, "end_pos": 1425, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079134", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1425", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779285328", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779285328" }, { "id": "rs1779285328", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1779285328" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1426, "end_pos": 1426, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079132", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1426", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749217346", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749217346" }, { "id": "rs749217346", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749217346" }, { "id": "rs749217346", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749217346#frequency_tab" }, { "id": "rs749217346", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749217346" } ], "glycoeffect": [], "start_pos": 1427, "end_pos": 1427, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079129", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1427", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749217346", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749217346" }, { "id": "rs749217346", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749217346" }, { "id": "rs749217346", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749217346#frequency_tab" }, { "id": "rs749217346", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749217346" } ], "glycoeffect": [], "start_pos": 1427, "end_pos": 1427, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079129", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1427", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1355379551", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355379551" }, { "id": "rs1355379551", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1355379551" } ], "glycoeffect": [], "start_pos": 1428, "end_pos": 1428, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079126", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1428", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760597086", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760597086" }, { "id": "rs760597086", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs760597086" } ], "glycoeffect": [], "start_pos": 1429, "end_pos": 1429, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079123", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1429", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1217559384", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1217559384" }, { "id": "rs1217559384", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1217559384" } ], "glycoeffect": [], "start_pos": 1429, "end_pos": 1429, "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079122", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1429", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 142, "end_pos": 142, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097428", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L142", "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": "rs758908709", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758908709" }, { "id": "rs758908709", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758908709" }, { "id": "rs758908709", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758908709" } ], "glycoeffect": [], "start_pos": 142, "end_pos": 142, "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097429", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L142", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1235420607", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235420607" }, { "id": "rs1235420607", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235420607" }, { "id": "rs1235420607", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1235420607" } ], "glycoeffect": [], "start_pos": 1433, "end_pos": 1433, "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079110", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1433", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs755953436", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755953436" }, { "id": "rs755953436", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755953436" }, { "id": "rs755953436", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755953436#frequency_tab" }, { "id": "rs755953436", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755953436" }, { "id": "rs755953436", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs755953436" } ], "glycoeffect": [], "start_pos": 1433, "end_pos": 1433, "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079111", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1433", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1195102797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1195102797" }, { "id": "rs1195102797", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1195102797" } ], "glycoeffect": [], "start_pos": 1434, "end_pos": 1434, "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079108", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1434", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1300419577", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1300419577" }, { "id": "rs1300419577", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1300419577" } ], "glycoeffect": [], "start_pos": 1435, "end_pos": 1435, "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079105", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1435", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750204851", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750204851" }, { "id": "rs750204851", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750204851" }, { "id": "rs750204851", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750204851" } ], "glycoeffect": [], "start_pos": 1436, "end_pos": 1436, "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079101", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1436", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1315071972", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1315071972" }, { "id": "rs1315071972", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1315071972#frequency_tab" } ], "glycoeffect": [], "start_pos": 1437, "end_pos": 1437, "sequence_org": "K", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079098", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1437", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1362162886", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1362162886" }, { "id": "rs1362162886", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1362162886" } ], "glycoeffect": [], "start_pos": 1437, "end_pos": 1437, "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079099", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1437", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1779281381", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779281381" }, { "id": "rs1779281381", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1779281381#frequency_tab" } ], "glycoeffect": [], "start_pos": 1438, "end_pos": 1438, "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079094", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1438", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767222442", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767222442" }, { "id": "rs767222442", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767222442" }, { "id": "rs767222442", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767222442" } ], "glycoeffect": [], "start_pos": 1439, "end_pos": 1439, "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079093", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1439", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2127293500", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127293500" }, { "id": "rs2127293500", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127293500" } ], "glycoeffect": [], "start_pos": 143, "end_pos": 143, "sequence_org": "C", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097426", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C143", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs1178974021", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1178974021" }, { "id": "rs1178974021", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1178974021" } ], "glycoeffect": [], "start_pos": 143, "end_pos": 143, "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097425", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "C143", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs756905708", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756905708" }, { "id": "rs756905708", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756905708" }, { "id": "rs756905708", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756905708#frequency_tab" }, { "id": "rs756905708", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756905708" } ], "glycoeffect": [], "start_pos": 1440, "end_pos": 1440, "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079090", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1440", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs762480960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762480960" }, { "id": "rs762480960", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs762480960" }, { "id": "rs762480960", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762480960" }, { "id": "rs762480960", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762480960#frequency_tab" }, { "id": "rs762480960", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762480960" } ], "glycoeffect": [], "start_pos": 1442, "end_pos": 1442, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079084", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "G1442", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs765829589", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765829589" }, { "id": "rs765829589", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765829589" }, { "id": "rs765829589", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765829589#frequency_tab" }, { "id": "rs765829589", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765829589" } ], "glycoeffect": [], "start_pos": 1445, "end_pos": 1445, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079075", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1445", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760049473", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760049473" }, { "id": "rs760049473", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760049473" }, { "id": "rs760049473", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760049473#frequency_tab" }, { "id": "rs760049473", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760049473" }, { "id": "rs760049473", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760049473" } ], "glycoeffect": [], "start_pos": 1446, "end_pos": 1446, "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079071", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1446", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779279102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779279102" }, { "id": "rs1779279102", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779279102" }, { "id": "rs1779279102", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1779279102" } ], "glycoeffect": [], "start_pos": 1446, "end_pos": 1446, "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079072", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1446", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1779279102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1779279102" }, { "id": "rs1779279102", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1779279102" } ], "glycoeffect": [], "start_pos": 1446, "end_pos": 1446, "sequence_org": "G", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079072", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1446", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1562847147", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1562847147" }, { "id": "rs1562847147", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1562847147" } ], "glycoeffect": [], "start_pos": 1447, "end_pos": 1447, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079069", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1447", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs372769933", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372769933" }, { "id": "rs372769933", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372769933" }, { "id": "rs372769933", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372769933#frequency_tab" }, { "id": "rs372769933", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372769933" } ], "glycoeffect": [], "start_pos": 1447, "end_pos": 1447, "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079068", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1447", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs936775313", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs936775313" }, { "id": "rs936775313", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs936775313#frequency_tab" }, { "id": "rs936775313", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs936775313" } ], "glycoeffect": [], "start_pos": 1448, "end_pos": 1448, "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079066", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1448", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs760174312", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760174312" }, { "id": "rs760174312", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760174312" }, { "id": "rs760174312", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760174312#frequency_tab" }, { "id": "rs760174312", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760174312" }, { "id": "rs760174312", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760174312" } ], "glycoeffect": [], "start_pos": 1448, "end_pos": 1448, "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079065", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1448", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs760174312", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760174312" }, { "id": "rs760174312", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760174312" }, { "id": "rs760174312", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760174312#frequency_tab" }, { "id": "rs760174312", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760174312" } ], "glycoeffect": [], "start_pos": 1448, "end_pos": 1448, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079065", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1448", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs936775313", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs936775313" }, { "id": "rs936775313", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs936775313#frequency_tab" } ], "glycoeffect": [], "start_pos": 1448, "end_pos": 1448, "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079066", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1448", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773445960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445960" }, { "id": "rs773445960", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445960" }, { "id": "rs773445960", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773445960#frequency_tab" }, { "id": "rs773445960", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773445960" } ], "glycoeffect": [], "start_pos": 1449, "end_pos": 1449, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079063", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1449", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773445960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445960" }, { "id": "rs773445960", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445960" }, { "id": "rs773445960", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773445960#frequency_tab" }, { "id": "rs773445960", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773445960" }, { "id": "rs773445960", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773445960" } ], "glycoeffect": [], "start_pos": 1449, "end_pos": 1449, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079063", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1449", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1237423218", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237423218" }, { "id": "rs1237423218", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237423218" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 144, "end_pos": 144, "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097422", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1237423218", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237423218" }, { "id": "rs1237423218", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237423218" } ], "glycoeffect": [], "start_pos": 144, "end_pos": 144, "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097422", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771493330", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771493330" }, { "id": "rs771493330", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771493330" }, { "id": "rs771493330", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771493330#frequency_tab" }, { "id": "rs771493330", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771493330" }, { "id": "rs771493330", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771493330" } ], "glycoeffect": [], "start_pos": 1451, "end_pos": 1451, "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079056", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1451", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs771493330", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771493330" }, { "id": "rs771493330", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771493330" }, { "id": "rs771493330", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771493330#frequency_tab" }, { "id": "rs771493330", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771493330" } ], "glycoeffect": [], "start_pos": 1451, "end_pos": 1451, "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079056", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1451", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs542750932", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs542750932" }, { "id": "rs542750932", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs542750932" }, { "id": "rs542750932", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs542750932#frequency_tab" }, { "id": "rs542750932", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs542750932" } ], "glycoeffect": [], "start_pos": 1452, "end_pos": 1452, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079054", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1452", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs542750932", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs542750932" }, { "id": "rs542750932", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs542750932" }, { "id": "rs542750932", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs542750932#frequency_tab" }, { "id": "rs542750932", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs542750932" }, { "id": "rs542750932", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs542750932" } ], "glycoeffect": [], "start_pos": 1452, "end_pos": 1452, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079054", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1452", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs267600973", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267600973" }, { "id": "rs267600973", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs267600973" }, { "id": "rs267600973", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs267600973" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1453, "end_pos": 1453, "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079050", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1453", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs374243353", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374243353" }, { "id": "rs374243353", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374243353" }, { "id": "rs374243353", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374243353#frequency_tab" }, { "id": "rs374243353", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs374243353" }, { "id": "rs374243353", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374243353" } ], "glycoeffect": [], "start_pos": 1454, "end_pos": 1454, "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "NC_000006.12", "chr_pos": "32079048", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "0.000020", "site_lbl": "A1454", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs572455281", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs572455281" }, { "id": "rs572455281", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs572455281" }, { "id": "rs572455281", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs572455281" }, { "id": "rs572455281", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs572455281#frequency_tab" }, { "id": "rs572455281", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs572455281" } ], "glycoeffect": [], "start_pos": 1455, "end_pos": 1455, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079045", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1455", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs572455281", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs572455281" }, { "id": "rs572455281", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs572455281" }, { "id": "rs572455281", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs572455281" }, { "id": "rs572455281", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs572455281#frequency_tab" }, { "id": "rs572455281", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs572455281" }, { "id": "rs572455281", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs572455281" } ], "glycoeffect": [], "start_pos": 1455, "end_pos": 1455, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079045", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1455", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs201153451", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201153451" }, { "id": "rs201153451", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201153451" }, { "id": "rs201153451", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201153451#frequency_tab" }, { "id": "rs201153451", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201153451" }, { "id": "rs201153451", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201153451" } ], "glycoeffect": [], "start_pos": 1457, "end_pos": 1457, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32079039", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1457", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs367922903", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367922903" }, { "id": "rs367922903", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367922903" }, { "id": "rs367922903", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs367922903#frequency_tab" }, { "id": "rs367922903", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367922903" } ], "glycoeffect": [], "start_pos": 1461, "end_pos": 1461, "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073947", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1461", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1033940667", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033940667" }, { "id": "rs1033940667", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1033940667#frequency_tab" }, { "id": "rs1033940667", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1033940667" } ], "glycoeffect": [], "start_pos": 1462, "end_pos": 1462, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073944", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1462", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1033940667", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033940667" }, { "id": "rs1033940667", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1033940667#frequency_tab" }, { "id": "rs1033940667", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1033940667" } ], "glycoeffect": [], "start_pos": 1462, "end_pos": 1462, "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073944", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1462", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778931526", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778931526" }, { "id": "rs1778931526", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778931526#frequency_tab" } ], "glycoeffect": [], "start_pos": 1463, "end_pos": 1463, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073941", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1463", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs761069340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761069340" }, { "id": "rs761069340", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761069340" }, { "id": "rs761069340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761069340" } ], "glycoeffect": [], "start_pos": 1464, "end_pos": 1464, "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073936", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1464", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1409770290", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1409770290" }, { "id": "rs1409770290", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1409770290" } ], "glycoeffect": [], "start_pos": 1464, "end_pos": 1464, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073938", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1464", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778930983", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778930983" } ], "glycoeffect": [], "start_pos": 1464, "end_pos": 1464, "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073938CTT", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1464", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1467218146", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467218146" }, { "id": "rs1467218146", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467218146#frequency_tab" }, { "id": "rs1467218146", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467218146" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1465, "end_pos": 1465, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073934", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1465", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1467218146", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467218146" }, { "id": "rs1467218146", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467218146#frequency_tab" }, { "id": "rs1467218146", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467218146" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1465, "end_pos": 1465, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073934", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1465", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772326782", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772326782" }, { "id": "rs772326782", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772326782" }, { "id": "rs772326782", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772326782" }, { "id": "rs772326782", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772326782" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1465, "end_pos": 1465, "sequence_org": "T", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073935", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1465", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1467218146", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467218146" }, { "id": "rs1467218146", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467218146#frequency_tab" }, { "id": "rs1467218146", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467218146" }, { "id": "rs772326782", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772326782" }, { "id": "rs772326782", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772326782" }, { "id": "rs772326782", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772326782" } ], "glycoeffect": [], "start_pos": 1465, "end_pos": 1465, "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073934", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1465", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1384747619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1384747619" }, { "id": "rs1384747619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1384747619" } ], "glycoeffect": [], "start_pos": 1466, "end_pos": 1466, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073931", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1466", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1213244609", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1213244609" }, { "id": "rs1213244609", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1213244609#frequency_tab" } ], "glycoeffect": [], "start_pos": 1467, "end_pos": 1467, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073929", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1467", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777196064", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777196064" }, { "id": "rs777196064", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777196064" }, { "id": "rs777196064", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777196064#frequency_tab" }, { "id": "rs777196064", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777196064" } ], "glycoeffect": [], "start_pos": 146, "end_pos": 146, "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097416", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H146", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1780476790", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780476790" }, { "id": "rs1780476790", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1780476790#frequency_tab" } ], "glycoeffect": [], "start_pos": 146, "end_pos": 146, "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097417", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H146", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781063575", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781063575" }, { "id": "rs781063575", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781063575" }, { "id": "rs781063575", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781063575#frequency_tab" }, { "id": "rs781063575", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781063575" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1471, "end_pos": 1471, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073916", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1471", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs745824476", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745824476" }, { "id": "rs745824476", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745824476" }, { "id": "rs745824476", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745824476#frequency_tab" }, { "id": "rs745824476", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745824476" } ], "glycoeffect": [], "start_pos": 1471, "end_pos": 1471, "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073917", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1471", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781063575", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781063575" }, { "id": "rs781063575", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781063575" }, { "id": "rs781063575", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781063575#frequency_tab" }, { "id": "rs781063575", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781063575" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1471, "end_pos": 1471, "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073916", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1471", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs374294912", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374294912" }, { "id": "rs374294912", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374294912" }, { "id": "rs374294912", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374294912#frequency_tab" }, { "id": "rs374294912", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374294912" }, { "id": "rs374294912", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs374294912" } ], "glycoeffect": [], "start_pos": 1472, "end_pos": 1472, "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073913", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1472", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs374294912", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374294912" }, { "id": "rs374294912", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374294912" }, { "id": "rs374294912", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374294912#frequency_tab" }, { "id": "rs374294912", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374294912" } ], "glycoeffect": [], "start_pos": 1472, "end_pos": 1472, "sequence_org": "P", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073913", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1472", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1358275258", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1358275258" }, { "id": "rs1358275258", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1358275258" } ], "glycoeffect": [], "start_pos": 1473, "end_pos": 1473, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073910", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1473", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2151921412", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2151921412" }, { "id": "rs2151921412", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2151921412" } ], "glycoeffect": [], "start_pos": 1475, "end_pos": 1475, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073905", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1475", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758078005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758078005" }, { "id": "rs758078005", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758078005" }, { "id": "rs758078005", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758078005#frequency_tab" }, { "id": "rs758078005", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758078005" } ], "glycoeffect": [], "start_pos": 1476, "end_pos": 1476, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073902", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1476", "disease": [ { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs752343940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752343940" }, { "id": "rs752343940", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752343940" }, { "id": "rs752343940", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752343940#frequency_tab" }, { "id": "rs752343940", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752343940" }, { "id": "rs752343940", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs752343940" } ], "glycoeffect": [], "start_pos": 1476, "end_pos": 1476, "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073901", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1476", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs752343940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752343940" }, { "id": "rs752343940", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752343940" }, { "id": "rs752343940", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752343940#frequency_tab" }, { "id": "rs752343940", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752343940" } ], "glycoeffect": [], "start_pos": 1476, "end_pos": 1476, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073901", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1476", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs540029834", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540029834" }, { "id": "rs540029834", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs540029834" }, { "id": "rs540029834", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540029834" }, { "id": "rs540029834", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs540029834#frequency_tab" }, { "id": "rs540029834", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs540029834" } ], "glycoeffect": [], "start_pos": 1478, "end_pos": 1478, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073896", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "G1478", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1041163540", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1041163540" }, { "id": "rs1041163540", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1041163540" } ], "glycoeffect": [], "start_pos": 147, "end_pos": 147, "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097414", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G147", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs1041163540", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1041163540" }, { "id": "rs1041163540", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1041163540" }, { "id": "rs1041163540", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1041163540" } ], "glycoeffect": [], "start_pos": 147, "end_pos": 147, "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097414", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G147", "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": "rs754436915", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754436915" }, { "id": "rs754436915", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754436915" }, { "id": "rs754436915", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754436915" } ], "glycoeffect": [], "start_pos": 1480, "end_pos": 1480, "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073890", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1480", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1353187688", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1353187688" }, { "id": "rs1353187688", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1353187688#frequency_tab" }, { "id": "rs1353187688", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1353187688" }, { "id": "rs1353187688", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1353187688" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1481, "end_pos": 1481, "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073887", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1481", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1778924199", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778924199" }, { "id": "rs1778924199", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778924199" } ], "glycoeffect": [], "start_pos": 1482, "end_pos": 1482, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073883", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1482", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs61740336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61740336" }, { "id": "rs61740336", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61740336" }, { "id": "rs61740336", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61740336" }, { "id": "rs61740336", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61740336#frequency_tab" }, { "id": "rs61740336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61740336" } ], "glycoeffect": [], "start_pos": 1482, "end_pos": 1482, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073884", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000588697", "site_lbl": "V1482", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778923990", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778923990" }, { "id": "rs1778923990", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778923990" } ], "glycoeffect": [], "start_pos": 1484, "end_pos": 1484, "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073877", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1484", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778923723", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778923723" }, { "id": "rs1778923723", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778923723#frequency_tab" } ], "glycoeffect": [], "start_pos": 1485, "end_pos": 1485, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073875", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1485", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1431114387", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1431114387" }, { "id": "rs1431114387", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1431114387" } ], "glycoeffect": [], "start_pos": 1487, "end_pos": 1487, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073869", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1487", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1431114387", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1431114387" }, { "id": "rs1431114387", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1431114387" } ], "glycoeffect": [], "start_pos": 1487, "end_pos": 1487, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073869", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1487", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1388282380", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1388282380" }, { "id": "rs1388282380", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1388282380#frequency_tab" } ], "glycoeffect": [], "start_pos": 1490, "end_pos": 1490, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073859", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1490", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778921960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778921960" }, { "id": "rs1778921960", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778921960" } ], "glycoeffect": [], "start_pos": 1492, "end_pos": 1492, "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073854", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1492", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1335061905", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1335061905" }, { "id": "rs1335061905", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1335061905#frequency_tab" }, { "id": "rs1335061905", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1335061905" } ], "glycoeffect": [], "start_pos": 1492, "end_pos": 1492, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073853", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1492", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1335061905", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1335061905" }, { "id": "rs1335061905", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1335061905#frequency_tab" }, { "id": "rs1335061905", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1335061905" } ], "glycoeffect": [], "start_pos": 1492, "end_pos": 1492, "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073853", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1492", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778921180", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778921180" }, { "id": "rs1778921180", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778921180" } ], "glycoeffect": [], "start_pos": 1494, "end_pos": 1494, "sequence_org": "W", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073848", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W1494", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs6910390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs6910390" }, { "id": "rs6910390", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs6910390" }, { "id": "rs6910390", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs6910390" }, { "id": "rs6910390", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs6910390#frequency_tab" }, { "id": "rs6910390", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs6910390" }, { "id": "rs6910390", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs6910390" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1495, "end_pos": 1495, "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073844", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1495", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs6910390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs6910390" }, { "id": "rs6910390", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs6910390" }, { "id": "rs6910390", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs6910390" }, { "id": "rs6910390", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs6910390#frequency_tab" }, { "id": "rs6910390", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs6910390" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1495, "end_pos": 1495, "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073844", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1495", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1380977388", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1380977388" }, { "id": "rs1380977388", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1380977388" }, { "id": "rs1380977388", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1380977388" } ], "glycoeffect": [], "start_pos": 1497, "end_pos": 1497, "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073839", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1497", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs374750804", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374750804" }, { "id": "rs374750804", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374750804" }, { "id": "rs374750804", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374750804#frequency_tab" }, { "id": "rs374750804", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374750804" }, { "id": "rs374750804", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs374750804" } ], "glycoeffect": [], "start_pos": 1498, "end_pos": 1498, "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073836", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1498", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1778919696", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778919696" }, { "id": "rs1778919696", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778919696#frequency_tab" } ], "glycoeffect": [], "start_pos": 1499, "end_pos": 1499, "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073832", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1499", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 14, "end_pos": 14, "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32098159", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L14", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs755462290", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755462290" }, { "id": "rs755462290", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755462290" }, { "id": "rs755462290", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755462290#frequency_tab" }, { "id": "rs755462290", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755462290" } ], "glycoeffect": [], "start_pos": 14, "end_pos": 14, "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32098159", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L14", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs932313112", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs932313112" }, { "id": "rs932313112", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs932313112#frequency_tab" }, { "id": "rs932313112", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs932313112" } ], "glycoeffect": [], "start_pos": 1500, "end_pos": 1500, "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073828", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1500", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1438776942", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438776942" }, { "id": "rs1438776942", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1438776942" } ], "glycoeffect": [], "start_pos": 1501, "end_pos": 1501, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073827", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1501", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1184896466", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1184896466" }, { "id": "rs1184896466", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1184896466" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1503, "end_pos": 1503, "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073821", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1503", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768750593", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768750593" }, { "id": "rs768750593", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768750593" }, { "id": "rs768750593", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768750593#frequency_tab" }, { "id": "rs768750593", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768750593" } ], "glycoeffect": [], "start_pos": 1504, "end_pos": 1504, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073818", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1504", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1473936921", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1473936921" }, { "id": "rs1473936921", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1473936921#frequency_tab" }, { "id": "rs1473936921", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1473936921" } ], "glycoeffect": [], "start_pos": 1505, "end_pos": 1505, "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073813", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1505", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs371430427", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371430427" }, { "id": "rs371430427", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371430427" }, { "id": "rs371430427", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371430427#frequency_tab" }, { "id": "rs371430427", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371430427" } ], "glycoeffect": [], "start_pos": 1505, "end_pos": 1505, "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073814", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1505", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778917880", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778917880" }, { "id": "rs1778917880", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778917880" } ], "glycoeffect": [], "start_pos": 1505, "end_pos": 1505, "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073815", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1505", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1218309816", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1218309816" }, { "id": "rs1218309816", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1218309816" } ], "glycoeffect": [], "start_pos": 1507, "end_pos": 1507, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073809", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1507", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778916994", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778916994" }, { "id": "rs1778916994", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778916994#frequency_tab" } ], "glycoeffect": [], "start_pos": 1507, "end_pos": 1507, "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073808", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1507", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778916771", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778916771" }, { "id": "rs1778916771", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778916771" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1508, "end_pos": 1508, "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073805", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1508", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 150, "end_pos": 150, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097403", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D150", "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": "rs1780476004", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780476004" }, { "id": "rs1780476004", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1780476004" } ], "glycoeffect": [], "start_pos": 150, "end_pos": 150, "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097405", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D150", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483616049", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483616049" } ], "glycoeffect": [], "start_pos": 1511, "end_pos": 1511, "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073796", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1511", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770885723", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770885723" }, { "id": "rs770885723", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770885723" }, { "id": "rs770885723", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770885723#frequency_tab" }, { "id": "rs770885723", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770885723" } ], "glycoeffect": [], "start_pos": 1512, "end_pos": 1512, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073794", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1512", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778916308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778916308" }, { "id": "rs1778916308", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778916308#frequency_tab" }, { "id": "rs1778916308", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778916308" } ], "glycoeffect": [], "start_pos": 1512, "end_pos": 1512, "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073793", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1512", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771301700", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771301700" }, { "id": "rs771301700", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771301700" }, { "id": "rs771301700", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771301700" }, { "id": "rs771301700", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771301700" } ], "glycoeffect": [], "start_pos": 1513, "end_pos": 1513, "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073791", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1513", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1277051308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1277051308" }, { "id": "rs1277051308", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1277051308" } ], "glycoeffect": [], "start_pos": 1514, "end_pos": 1514, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073788", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1514", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1437665984", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437665984" }, { "id": "rs1437665984", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437665984" } ], "glycoeffect": [], "start_pos": 1515, "end_pos": 1515, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073785", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1515", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1365287561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365287561" }, { "id": "rs1365287561", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1365287561" } ], "glycoeffect": [], "start_pos": 1516, "end_pos": 1516, "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073782", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1516", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778914982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778914982" }, { "id": "rs1778914982", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778914982" } ], "glycoeffect": [], "start_pos": 1517, "end_pos": 1517, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073779", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1517", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376280627", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376280627" }, { "id": "rs376280627", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376280627" }, { "id": "rs376280627", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376280627#frequency_tab" }, { "id": "rs376280627", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376280627" } ], "glycoeffect": [], "start_pos": 1518, "end_pos": 1518, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073776", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1518", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778913854", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778913854" }, { "id": "rs1778913854", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778913854" } ], "glycoeffect": [], "start_pos": 1519, "end_pos": 1519, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073773", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1519", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs373057447", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373057447" }, { "id": "rs373057447", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373057447" }, { "id": "rs373057447", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373057447#frequency_tab" }, { "id": "rs373057447", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373057447" } ], "glycoeffect": [], "start_pos": 1519, "end_pos": 1519, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073772", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1519", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 151, "end_pos": 151, "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097402", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L151", "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": "rs146120469", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146120469" }, { "id": "rs146120469", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146120469" }, { "id": "rs146120469", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146120469" }, { "id": "rs146120469", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146120469#frequency_tab" }, { "id": "rs146120469", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146120469" } ], "glycoeffect": [], "start_pos": 1521, "end_pos": 1521, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073766", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.00412088", "site_lbl": "A1521", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs868656534", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868656534" }, { "id": "rs868656534", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs868656534" } ], "glycoeffect": [], "start_pos": 1522, "end_pos": 1522, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073764", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1522", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753387674", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753387674" }, { "id": "rs753387674", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753387674" }, { "id": "rs753387674", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753387674" } ], "glycoeffect": [], "start_pos": 1524, "end_pos": 1524, "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073758", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1524", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1488403436", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1488403436" }, { "id": "rs1488403436", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1488403436" } ], "glycoeffect": [], "start_pos": 1524, "end_pos": 1524, "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073756", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1524", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779751914", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779751914" }, { "id": "rs779751914", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779751914#frequency_tab" }, { "id": "rs779751914", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779751914" }, { "id": "rs779751914", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs779751914" } ], "glycoeffect": [], "start_pos": 1525, "end_pos": 1525, "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073755", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1525", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs780494267", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780494267" }, { "id": "rs780494267", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780494267" }, { "id": "rs780494267", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780494267#frequency_tab" }, { "id": "rs780494267", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780494267" } ], "glycoeffect": [], "start_pos": 1525, "end_pos": 1525, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073754", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1525", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs780494267", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780494267" }, { "id": "rs780494267", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780494267" }, { "id": "rs780494267", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780494267#frequency_tab" }, { "id": "rs780494267", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780494267" } ], "glycoeffect": [], "start_pos": 1525, "end_pos": 1525, "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073754", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1525", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1213041181", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1213041181" }, { "id": "rs1213041181", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1213041181" } ], "glycoeffect": [], "start_pos": 1527, "end_pos": 1527, "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073749", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1527", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs987362626", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs987362626" }, { "id": "rs987362626", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs987362626#frequency_tab" }, { "id": "rs987362626", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs987362626" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1528, "end_pos": 1528, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073745", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1528", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778909961", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778909961" }, { "id": "rs1778909961", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778909961" } ], "glycoeffect": [], "start_pos": 1529, "end_pos": 1529, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073742", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1529", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1243583800", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243583800" }, { "id": "rs1243583800", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1243583800#frequency_tab" }, { "id": "rs1243583800", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243583800" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 152, "end_pos": 152, "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097399", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S152", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483614935", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483614935" } ], "glycoeffect": [], "start_pos": 1534, "end_pos": 1534, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073727", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1534", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767947459", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767947459" }, { "id": "rs767947459", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767947459" }, { "id": "rs767947459", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767947459" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1538, "end_pos": 1538, "sequence_org": "Y", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073716", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1538", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs552798448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552798448" }, { "id": "rs552798448", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs552798448" }, { "id": "rs552798448", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552798448" }, { "id": "rs552798448", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs552798448#frequency_tab" }, { "id": "rs552798448", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs552798448" } ], "glycoeffect": [], "start_pos": 153, "end_pos": 153, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097396", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R153", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs552798448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552798448" }, { "id": "rs552798448", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs552798448" }, { "id": "rs552798448", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552798448" }, { "id": "rs552798448", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs552798448#frequency_tab" }, { "id": "rs552798448", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs552798448" } ], "glycoeffect": [], "start_pos": 153, "end_pos": 153, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097396", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R153", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773546748", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773546748" }, { "id": "rs773546748", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773546748" }, { "id": "rs773546748", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773546748#frequency_tab" }, { "id": "rs773546748", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773546748" }, { "id": "rs773546748", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773546748" } ], "glycoeffect": [], "start_pos": 153, "end_pos": 153, "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097395", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R153", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs773546748", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773546748" }, { "id": "rs773546748", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773546748" }, { "id": "rs773546748", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773546748#frequency_tab" }, { "id": "rs773546748", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773546748" } ], "glycoeffect": [], "start_pos": 153, "end_pos": 153, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097395", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R153", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1362941338", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1362941338" }, { "id": "rs1362941338", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1362941338" } ], "glycoeffect": [], "start_pos": 1540, "end_pos": 1540, "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073709", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1540", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778908775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778908775" }, { "id": "rs1778908775", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778908775#frequency_tab" }, { "id": "rs1778908775", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778908775" }, { "id": "rs1778908775", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1778908775" } ], "glycoeffect": [], "start_pos": 1540, "end_pos": 1540, "sequence_org": "M", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073710", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1540", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs757573988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757573988" }, { "id": "rs757573988", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757573988" }, { "id": "rs757573988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757573988" } ], "glycoeffect": [], "start_pos": 1541, "end_pos": 1541, "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073706", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1541", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs751815516", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751815516" }, { "id": "rs751815516", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751815516" }, { "id": "rs751815516", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751815516" } ], "glycoeffect": [], "start_pos": 1542, "end_pos": 1542, "sequence_org": "M", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073704", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1542", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1186563015", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1186563015" }, { "id": "rs1186563015", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1186563015#frequency_tab" } ], "glycoeffect": [], "start_pos": 1542, "end_pos": 1542, "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073703", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1542", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1360920030", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360920030" }, { "id": "rs1360920030", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360920030" }, { "id": "rs1360920030", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1360920030" } ], "glycoeffect": [], "start_pos": 1544, "end_pos": 1544, "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073698", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1544", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1778907501", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778907501" }, { "id": "rs1778907501", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778907501" } ], "glycoeffect": [], "start_pos": 1546, "end_pos": 1546, "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073692", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1546", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1025025117", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1025025117" }, { "id": "rs1025025117", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1025025117#frequency_tab" }, { "id": "rs1025025117", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1025025117" } ], "glycoeffect": [], "start_pos": 1547, "end_pos": 1547, "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073689", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1547", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1025025117", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1025025117" }, { "id": "rs1025025117", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1025025117#frequency_tab" }, { "id": "rs1025025117", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1025025117" } ], "glycoeffect": [], "start_pos": 1547, "end_pos": 1547, "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073689", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1547", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764276191", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764276191" }, { "id": "rs764276191", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764276191" }, { "id": "rs764276191", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764276191" } ], "glycoeffect": [], "start_pos": 1548, "end_pos": 1548, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073685", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1548", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2151921014", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2151921014" }, { "id": "rs2151921014", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2151921014" } ], "glycoeffect": [], "start_pos": 1549, "end_pos": 1549, "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073683", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1549", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 154, "end_pos": 154, "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097392", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "C154", "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": "rs865873272", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs865873272" }, { "id": "rs865873272", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs865873272" } ], "glycoeffect": [], "start_pos": 1550, "end_pos": 1550, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073680", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1550", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763075781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763075781" }, { "id": "rs763075781", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763075781" }, { "id": "rs763075781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763075781#frequency_tab" }, { "id": "rs763075781", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763075781" }, { "id": "rs763075781", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs763075781" } ], "glycoeffect": [], "start_pos": 1550, "end_pos": 1550, "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073679", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1550", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs763075781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763075781" }, { "id": "rs763075781", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763075781" }, { "id": "rs763075781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763075781#frequency_tab" }, { "id": "rs763075781", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763075781" } ], "glycoeffect": [], "start_pos": 1550, "end_pos": 1550, "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073679", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1550", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1430157478", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1430157478" }, { "id": "rs1430157478", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1430157478#frequency_tab" }, { "id": "rs1430157478", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1430157478" } ], "glycoeffect": [], "start_pos": 1551, "end_pos": 1551, "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073675", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1551", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778906089", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778906089" }, { "id": "rs1778906089", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778906089#frequency_tab" }, { "id": "rs1778906089", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778906089" } ], "glycoeffect": [], "start_pos": 1551, "end_pos": 1551, "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073677", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1551", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775647752", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775647752" }, { "id": "rs775647752", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775647752" }, { "id": "rs775647752", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775647752#frequency_tab" }, { "id": "rs775647752", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775647752" } ], "glycoeffect": [], "start_pos": 1552, "end_pos": 1552, "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073673", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1552", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1477986984", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1477986984" }, { "id": "rs1477986984", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1477986984" }, { "id": "rs1477986984", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1477986984" } ], "glycoeffect": [], "start_pos": 1552, "end_pos": 1552, "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073674", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1552", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1483974773", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483974773" }, { "id": "rs1483974773", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1483974773" } ], "glycoeffect": [], "start_pos": 1553, "end_pos": 1553, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073671", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1553", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778904633", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778904633" }, { "id": "rs1778904633", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778904633" }, { "id": "rs1778904633", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1778904633" } ], "glycoeffect": [], "start_pos": 1553, "end_pos": 1553, "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073670", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1553", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1483974773", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483974773" }, { "id": "rs1483974773", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1483974773" } ], "glycoeffect": [], "start_pos": 1553, "end_pos": 1553, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073671", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1553", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779291187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779291187" }, { "id": "rs779291187", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779291187" }, { "id": "rs779291187", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779291187#frequency_tab" }, { "id": "rs779291187", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779291187" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1555, "end_pos": 1555, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073664", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1555", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771942722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771942722" }, { "id": "rs771942722", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771942722" }, { "id": "rs771942722", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771942722#frequency_tab" }, { "id": "rs771942722", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771942722" } ], "glycoeffect": [], "start_pos": 1557, "end_pos": 1557, "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073658", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1557", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1295158109", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1295158109" }, { "id": "rs1295158109", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1295158109" } ], "glycoeffect": [], "start_pos": 1558, "end_pos": 1558, "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073655", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1558", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747934395", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747934395" }, { "id": "rs747934395", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747934395" }, { "id": "rs747934395", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747934395" } ], "glycoeffect": [], "start_pos": 1558, "end_pos": 1558, "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073656", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1558", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1381514646", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381514646" }, { "id": "rs1381514646", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1381514646#frequency_tab" }, { "id": "rs1381514646", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381514646" } ], "glycoeffect": [], "start_pos": 1559, "end_pos": 1559, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073653", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1559", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772323777", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772323777" }, { "id": "rs772323777", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772323777" }, { "id": "rs772323777", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772323777" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 155, "end_pos": 155, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097390", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T155", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs535714494", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs535714494" }, { "id": "rs535714494", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs535714494" }, { "id": "rs535714494", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs535714494#frequency_tab" }, { "id": "rs535714494", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs535714494" }, { "id": "rs535714494", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs535714494" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1560, "end_pos": 1560, "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073649", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1560", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1365818147", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365818147" }, { "id": "rs1365818147", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1365818147" } ], "glycoeffect": [], "start_pos": 1561, "end_pos": 1561, "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072298", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1561", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748880911", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748880911" }, { "id": "rs748880911", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748880911" }, { "id": "rs748880911", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748880911#frequency_tab" }, { "id": "rs748880911", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748880911" } ], "glycoeffect": [], "start_pos": 1561, "end_pos": 1561, "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073647", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1561", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748880911", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748880911" }, { "id": "rs748880911", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748880911" }, { "id": "rs748880911", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748880911#frequency_tab" }, { "id": "rs748880911", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748880911" } ], "glycoeffect": [], "start_pos": 1561, "end_pos": 1561, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32073647", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1561", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1562, "end_pos": 1562, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072296", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1562", "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": "rs906389854", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs906389854" }, { "id": "rs906389854", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs906389854" } ], "glycoeffect": [], "start_pos": 1563, "end_pos": 1563, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072292", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1563", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1442269562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1442269562" }, { "id": "rs1442269562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1442269562" } ], "glycoeffect": [], "start_pos": 1564, "end_pos": 1564, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072289", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1564", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1564, "end_pos": 1564, "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072289", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1564", "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": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs767549927", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767549927" }, { "id": "rs767549927", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767549927" }, { "id": "rs767549927", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767549927" } ], "glycoeffect": [], "start_pos": 1564, "end_pos": 1564, "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072290", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1564", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs199784025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199784025" }, { "id": "rs199784025", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199784025" }, { "id": "rs199784025", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199784025#frequency_tab" }, { "id": "rs199784025", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199784025" } ], "glycoeffect": [], "start_pos": 1565, "end_pos": 1565, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072286", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1565", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199784025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199784025" }, { "id": "rs199784025", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199784025" }, { "id": "rs199784025", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199784025#frequency_tab" }, { "id": "rs199784025", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199784025" } ], "glycoeffect": [], "start_pos": 1565, "end_pos": 1565, "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072286", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1565", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778824128", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778824128" }, { "id": "rs1778824128", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778824128" } ], "glycoeffect": [], "start_pos": 1567, "end_pos": 1567, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072280", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1567", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778823970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778823970" }, { "id": "rs1778823970", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778823970#frequency_tab" } ], "glycoeffect": [], "start_pos": 1568, "end_pos": 1568, "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072277", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1568", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs1445119291", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1445119291" }, { "id": "rs1445119291", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1445119291" }, { "id": "rs1445119291", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1445119291" } ], "glycoeffect": [], "start_pos": 156, "end_pos": 156, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097385", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "C156", "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": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs1331242504", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1331242504" }, { "id": "rs1331242504", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1331242504" }, { "id": "rs1331242504", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1331242504" } ], "glycoeffect": [], "start_pos": 156, "end_pos": 156, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097386", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "C156", "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": "rs774295104", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774295104" }, { "id": "rs774295104", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774295104" }, { "id": "rs774295104", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774295104" } ], "glycoeffect": [], "start_pos": 1571, "end_pos": 1571, "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072268", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1571", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs374179831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374179831" }, { "id": "rs374179831", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374179831#frequency_tab" }, { "id": "rs374179831", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374179831" } ], "glycoeffect": [], "start_pos": 1571, "end_pos": 1571, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072269", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1571", "disease": [ { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs774295104", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774295104" }, { "id": "rs774295104", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774295104" }, { "id": "rs774295104", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774295104" } ], "glycoeffect": [], "start_pos": 1571, "end_pos": 1571, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072268", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1571", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1572, "end_pos": 1572, "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072265", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1572", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1194439673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194439673" }, { "id": "rs1194439673", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194439673#frequency_tab" }, { "id": "rs1194439673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194439673" } ], "glycoeffect": [], "start_pos": 1573, "end_pos": 1573, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072263", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1573", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1489647639", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1489647639" }, { "id": "rs1489647639", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1489647639#frequency_tab" }, { "id": "rs1489647639", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1489647639" } ], "glycoeffect": [], "start_pos": 1573, "end_pos": 1573, "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072261", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1573", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768512703", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768512703" }, { "id": "rs768512703", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768512703" }, { "id": "rs768512703", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768512703" } ], "glycoeffect": [], "start_pos": 1574, "end_pos": 1574, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072260", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1574", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778821796", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778821796" }, { "id": "rs1778821796", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778821796" } ], "glycoeffect": [], "start_pos": 1574, "end_pos": 1574, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072259", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1574", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1575, "end_pos": 1575, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072256", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1575", "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": "rs748991428", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748991428" }, { "id": "rs748991428", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748991428" }, { "id": "rs748991428", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748991428" } ], "glycoeffect": [], "start_pos": 1578, "end_pos": 1578, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072248", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1578", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs774965296", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774965296" }, { "id": "rs774965296", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774965296" }, { "id": "rs774965296", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774965296#frequency_tab" }, { "id": "rs774965296", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774965296" }, { "id": "rs774965296", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774965296" } ], "glycoeffect": [], "start_pos": 1579, "end_pos": 1579, "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072245", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1579", "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" ] }, { "evidence": [ { "id": "rs142266956", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142266956" }, { "id": "rs142266956", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142266956" }, { "id": "rs142266956", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142266956" }, { "id": "rs142266956", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142266956#frequency_tab" }, { "id": "rs142266956", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142266956" } ], "glycoeffect": [], "start_pos": 1579, "end_pos": 1579, "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072244", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1579", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774965296", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774965296" }, { "id": "rs774965296", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774965296" }, { "id": "rs774965296", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774965296#frequency_tab" }, { "id": "rs774965296", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774965296" } ], "glycoeffect": [], "start_pos": 1579, "end_pos": 1579, "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072245", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1579", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 157, "end_pos": 157, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097383", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S157", "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": "rs1170691445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170691445" }, { "id": "rs1170691445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170691445" } ], "glycoeffect": [], "start_pos": 1581, "end_pos": 1581, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072238", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1581", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1582, "end_pos": 1582, "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072235", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E1582", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1009885940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009885940" }, { "id": "rs1009885940", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1009885940" } ], "glycoeffect": [], "start_pos": 1582, "end_pos": 1582, "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072235", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1582", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1584, "end_pos": 1584, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072229", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1584", "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": "rs745343270", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745343270" }, { "id": "rs745343270", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745343270" }, { "id": "rs745343270", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745343270#frequency_tab" }, { "id": "rs745343270", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745343270" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1586, "end_pos": 1586, "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072223", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1586", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs745343270", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745343270" }, { "id": "rs745343270", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745343270" }, { "id": "rs745343270", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745343270#frequency_tab" }, { "id": "rs745343270", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745343270" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1586, "end_pos": 1586, "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072223", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1586", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757753814", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757753814" }, { "id": "rs757753814", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757753814" }, { "id": "rs757753814", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757753814" } ], "glycoeffect": [], "start_pos": 1587, "end_pos": 1587, "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072220", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1587", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs867305770", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867305770" }, { "id": "rs867305770", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs867305770#frequency_tab" } ], "glycoeffect": [], "start_pos": 1588, "end_pos": 1588, "sequence_org": "I", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072217", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1588", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs867305770", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867305770" }, { "id": "rs867305770", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs867305770#frequency_tab" } ], "glycoeffect": [], "start_pos": 1588, "end_pos": 1588, "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072217", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1588", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs569747700", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs569747700" }, { "id": "rs569747700", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs569747700" }, { "id": "rs569747700", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs569747700" }, { "id": "rs569747700", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs569747700#frequency_tab" }, { "id": "rs569747700", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs569747700" }, { "id": "rs569747700", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs569747700" } ], "glycoeffect": [], "start_pos": 1588, "end_pos": 1588, "sequence_org": "I", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072218", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000784929", "site_lbl": "I1588", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs2151919300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2151919300" }, { "id": "rs2151919300", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2151919300" } ], "glycoeffect": [], "start_pos": 1589, "end_pos": 1589, "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072214", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1589", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1389734692", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1389734692" }, { "id": "rs1389734692", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1389734692#frequency_tab" } ], "glycoeffect": [], "start_pos": 1590, "end_pos": 1590, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072212", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1590", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1437696599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437696599" }, { "id": "rs1437696599", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1437696599#frequency_tab" }, { "id": "rs1437696599", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437696599" } ], "glycoeffect": [], "start_pos": 1590, "end_pos": 1590, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072211", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1590", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1437696599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437696599" }, { "id": "rs1437696599", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1437696599#frequency_tab" }, { "id": "rs1437696599", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437696599" } ], "glycoeffect": [], "start_pos": 1590, "end_pos": 1590, "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072211", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1590", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs891472357", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs891472357" }, { "id": "rs891472357", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs891472357#frequency_tab" }, { "id": "rs891472357", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs891472357" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1592, "end_pos": 1592, "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072205", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1592", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs891472357", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs891472357" }, { "id": "rs891472357", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs891472357#frequency_tab" }, { "id": "rs891472357", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs891472357" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1592, "end_pos": 1592, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072205", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1592", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483604684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483604684" } ], "glycoeffect": [], "start_pos": 1593, "end_pos": 1593, "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072201CA", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1593", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1594, "end_pos": 1594, "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072200", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1594", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1363756520", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363756520" }, { "id": "rs1363756520", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363756520" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1596, "end_pos": 1596, "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072193", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1596", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1597, "end_pos": 1597, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072190", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W1597", "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": "rs1778816402", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778816402" }, { "id": "rs1778816402", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778816402" } ], "glycoeffect": [], "start_pos": 1597, "end_pos": 1597, "sequence_org": "W", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072191", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W1597", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1599, "end_pos": 1599, "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072184", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V1599", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 159, "end_pos": 159, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097378", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E159", "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": "rs1192231411", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1192231411" }, { "id": "rs1192231411", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1192231411#frequency_tab" }, { "id": "rs1192231411", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1192231411" } ], "glycoeffect": [], "start_pos": 1600, "end_pos": 1600, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072182", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1600", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1475833749", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475833749" }, { "id": "rs1475833749", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1475833749" } ], "glycoeffect": [], "start_pos": 1601, "end_pos": 1601, "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072179", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1601", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778815272", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778815272" } ], "glycoeffect": [], "start_pos": 1601, "end_pos": 1601, "sequence_org": "E", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072178", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1601", "disease": [ { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1778815272", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778815272" }, { "id": "rs1778815272", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778815272#frequency_tab" } ], "glycoeffect": [], "start_pos": 1601, "end_pos": 1601, "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072178", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1601", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1604, "end_pos": 1604, "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072169", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F1604", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs554703532", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs554703532" }, { "id": "rs554703532", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs554703532" }, { "id": "rs554703532", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs554703532" }, { "id": "rs554703532", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs554703532" }, { "id": "rs536054720", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536054720" }, { "id": "rs536054720", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536054720" }, { "id": "rs536054720", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536054720" }, { "id": "rs536054720", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs536054720#frequency_tab" }, { "id": "rs536054720", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs536054720" } ], "glycoeffect": [], "start_pos": 1604, "end_pos": 1604, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072170", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "F1604", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs565606966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565606966" }, { "id": "rs565606966", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs565606966" }, { "id": "rs565606966", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565606966" }, { "id": "rs565606966", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs565606966#frequency_tab" }, { "id": "rs565606966", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs565606966" }, { "id": "rs565606966", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs565606966" } ], "glycoeffect": [], "start_pos": 1605, "end_pos": 1605, "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072167", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1605", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1047141638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047141638" }, { "id": "rs1047141638", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1047141638#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1606, "end_pos": 1606, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072163", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1606", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753860861", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753860861" }, { "id": "rs753860861", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753860861" }, { "id": "rs753860861", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753860861" } ], "glycoeffect": [], "start_pos": 1607, "end_pos": 1607, "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072160", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1607", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778813161", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778813161" }, { "id": "rs1778813161", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778813161" }, { "id": "rs1778813161", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1778813161" } ], "glycoeffect": [], "start_pos": 1608, "end_pos": 1608, "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072158", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1608", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1304232078", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1304232078" }, { "id": "rs1304232078", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1304232078#frequency_tab" }, { "id": "rs1304232078", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1304232078" } ], "glycoeffect": [], "start_pos": 160, "end_pos": 160, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097375", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P160", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 160, "end_pos": 160, "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097375", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P160", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1610, "end_pos": 1610, "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072152", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q1610", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1778812534", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778812534" }, { "id": "rs1778812534", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778812534" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1611, "end_pos": 1611, "sequence_org": "Y", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072147", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1611", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778812721", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778812721" }, { "id": "rs1778812721", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778812721#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1611, "end_pos": 1611, "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072149", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1611", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1613, "end_pos": 1613, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072141", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1613", "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": "rs547312711", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547312711" }, { "id": "rs547312711", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547312711" }, { "id": "rs547312711", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs547312711" } ], "glycoeffect": [], "start_pos": 1613, "end_pos": 1613, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072143", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1613", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs751491483", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751491483" }, { "id": "rs751491483", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751491483" }, { "id": "rs751491483", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751491483#frequency_tab" }, { "id": "rs751491483", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751491483" } ], "glycoeffect": [], "start_pos": 1616, "end_pos": 1616, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072134", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1616", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1244716570", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1244716570" }, { "id": "rs1244716570", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1244716570" } ], "glycoeffect": [], "start_pos": 1617, "end_pos": 1617, "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072129", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1617", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1617, "end_pos": 1617, "subjects_tested": "2003", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072130", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q1617", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1235302367", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235302367" }, { "id": "rs1235302367", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235302367" } ], "glycoeffect": [], "start_pos": 1618, "end_pos": 1618, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072127", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1618", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1324056823", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324056823" }, { "id": "rs1324056823", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324056823" } ], "glycoeffect": [], "start_pos": 1619, "end_pos": 1619, "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072124", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1619", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs2127293410", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2127293410" }, { "id": "rs2127293410", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2127293410" } ], "glycoeffect": [], "start_pos": 161, "end_pos": 161, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097371", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G161", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778810746", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778810746" }, { "id": "rs1778810746", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778810746" } ], "glycoeffect": [], "start_pos": 1620, "end_pos": 1620, "sequence_org": "V", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072121", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1620", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs372387718", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372387718" }, { "id": "rs372387718", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372387718" }, { "id": "rs372387718", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372387718#frequency_tab" }, { "id": "rs372387718", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372387718" } ], "glycoeffect": [], "start_pos": 1621, "end_pos": 1621, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072119", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1621", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs372387718", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372387718" }, { "id": "rs372387718", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372387718" }, { "id": "rs372387718", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372387718#frequency_tab" }, { "id": "rs372387718", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372387718" } ], "glycoeffect": [], "start_pos": 1621, "end_pos": 1621, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072119", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1621", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs549598494", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549598494" }, { "id": "rs549598494", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549598494" }, { "id": "rs549598494", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549598494" }, { "id": "rs549598494", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549598494#frequency_tab" }, { "id": "rs549598494", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549598494" } ], "glycoeffect": [], "start_pos": 1623, "end_pos": 1623, "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072113", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "V1623", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs549598494", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549598494" }, { "id": "rs549598494", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549598494" }, { "id": "rs549598494", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549598494" }, { "id": "rs549598494", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549598494#frequency_tab" }, { "id": "rs549598494", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549598494" } ], "glycoeffect": [], "start_pos": 1623, "end_pos": 1623, "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072113", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "V1623", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776121487", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776121487" }, { "id": "rs776121487", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776121487" }, { "id": "rs776121487", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776121487" } ], "glycoeffect": [], "start_pos": 1624, "end_pos": 1624, "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072109", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1624", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778809080", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778809080" }, { "id": "rs1778809080", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778809080#frequency_tab" }, { "id": "rs1778809080", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778809080" } ], "glycoeffect": [], "start_pos": 1625, "end_pos": 1625, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072107", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1625", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1627, "end_pos": 1627, "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072099", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q1627", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs778225485", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778225485" }, { "id": "rs778225485", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778225485" }, { "id": "rs778225485", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778225485#frequency_tab" }, { "id": "rs778225485", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778225485" } ], "glycoeffect": [], "start_pos": 1628, "end_pos": 1628, "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072097", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1628", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs747549013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747549013" }, { "id": "rs747549013", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747549013" }, { "id": "rs747549013", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747549013#frequency_tab" }, { "id": "rs747549013", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747549013" }, { "id": "rs747549013", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs747549013" } ], "glycoeffect": [], "start_pos": 1628, "end_pos": 1628, "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072098", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1628", "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" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs78493656", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs78493656" }, { "id": "rs78493656", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs78493656" }, { "id": "rs78493656", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs78493656" }, { "id": "rs78493656", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs78493656#frequency_tab" }, { "id": "rs78493656", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs78493656" }, { "id": "rs78493656", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs78493656" } ], "glycoeffect": [], "start_pos": 1629, "end_pos": 1629, "subjects_tested": "606", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072095", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E1629", "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 162, "end_pos": 162, "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097368", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W162", "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": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 162, "end_pos": 162, "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097369", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W162", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1778807529", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778807529" }, { "id": "rs1778807529", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778807529#frequency_tab" } ], "glycoeffect": [], "start_pos": 1630, "end_pos": 1630, "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072092", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1630", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2151919102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2151919102" }, { "id": "rs2151919102", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2151919102" } ], "glycoeffect": [], "start_pos": 1630, "end_pos": 1630, "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072091", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V1630", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778807144", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778807144" }, { "id": "rs1778807144", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778807144" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1631, "end_pos": 1631, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072089", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1631", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483603372", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483603372" } ], "glycoeffect": [], "start_pos": 1632, "end_pos": 1632, "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072084", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1632", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766602645", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766602645" }, { "id": "rs766602645", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766602645" }, { "id": "rs766602645", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766602645#frequency_tab" }, { "id": "rs766602645", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766602645" } ], "glycoeffect": [], "start_pos": 1632, "end_pos": 1632, "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072086", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1632", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ] }, { "evidence": [ { "id": "rs1778806523", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778806523" }, { "id": "rs1778806523", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1778806523#frequency_tab" } ], "glycoeffect": [], "start_pos": 1633, "end_pos": 1633, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072082", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1633", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1633, "end_pos": 1633, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072083", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1633", "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": "rs1349601739", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349601739" }, { "id": "rs1349601739", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1349601739" } ], "glycoeffect": [], "start_pos": 1634, "end_pos": 1634, "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072080", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1634", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs992498462", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992498462" }, { "id": "rs992498462", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992498462#frequency_tab" }, { "id": "rs992498462", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992498462" } ], "glycoeffect": [], "start_pos": 1635, "end_pos": 1635, "sequence_org": "L", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072077", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1635", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755161052", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755161052" }, { "id": "rs755161052", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755161052" }, { "id": "rs755161052", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755161052" } ], "glycoeffect": [], "start_pos": 1636, "end_pos": 1636, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072074", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1636", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1636, "end_pos": 1636, "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072074", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "E1636", "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": "rs1194113762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194113762" }, { "id": "rs1194113762", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194113762#frequency_tab" }, { "id": "rs1194113762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194113762" } ], "glycoeffect": [], "start_pos": 1637, "end_pos": 1637, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072071", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1637", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2483603209", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2483603209" } ], "glycoeffect": [], "start_pos": 1637, "end_pos": 1637, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072070", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1637", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1194113762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194113762" }, { "id": "rs1194113762", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194113762#frequency_tab" }, { "id": "rs1194113762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194113762" } ], "glycoeffect": [], "start_pos": 1637, "end_pos": 1637, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072071", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1637", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs370049143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370049143" }, { "id": "rs370049143", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370049143" }, { "id": "rs370049143", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370049143#frequency_tab" }, { "id": "rs370049143", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370049143" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1638, "end_pos": 1638, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072067", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1638", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs780301586", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780301586" }, { "id": "rs780301586", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780301586" }, { "id": "rs780301586", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780301586#frequency_tab" }, { "id": "rs780301586", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780301586" } ], "glycoeffect": [], "start_pos": 1639, "end_pos": 1639, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072065", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1639", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs780301586", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780301586" }, { "id": "rs780301586", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780301586" }, { "id": "rs780301586", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780301586#frequency_tab" }, { "id": "rs780301586", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780301586" } ], "glycoeffect": [], "start_pos": 1639, "end_pos": 1639, "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072065", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1639", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs756221645", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756221645" }, { "id": "rs756221645", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756221645" }, { "id": "rs756221645", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756221645#frequency_tab" }, { "id": "rs756221645", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756221645" } ], "glycoeffect": [], "start_pos": 1639, "end_pos": 1639, "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072064", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1639", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1639, "end_pos": 1639, "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072064", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1639", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1780473824", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780473824" }, { "id": "rs1780473824", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1780473824#frequency_tab" } ], "glycoeffect": [], "start_pos": 163, "end_pos": 163, "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097365", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G163", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1780473824", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1780473824" }, { "id": "rs1780473824", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1780473824#frequency_tab" } ], "glycoeffect": [], "start_pos": 163, "end_pos": 163, "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097365", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G163", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 163, "end_pos": 163, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32097366", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G163", "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": "rs374991528", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374991528" }, { "id": "rs374991528", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374991528" }, { "id": "rs374991528", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374991528#frequency_tab" }, { "id": "rs374991528", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374991528" } ], "glycoeffect": [], "start_pos": 1640, "end_pos": 1640, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072062", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1640", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1640, "end_pos": 1640, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072060", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1640", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs374991528", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374991528" }, { "id": "rs374991528", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374991528" }, { "id": "rs374991528", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374991528#frequency_tab" }, { "id": "rs374991528", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374991528" } ], "glycoeffect": [], "start_pos": 1640, "end_pos": 1640, "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072062", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1640", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1262353356", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262353356" }, { "id": "rs1262353356", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262353356" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1641, "end_pos": 1641, "sequence_org": "Y", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072057", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1641", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764100849", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764100849" }, { "id": "rs764100849", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764100849" }, { "id": "rs764100849", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764100849#frequency_tab" }, { "id": "rs764100849", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764100849" } ], "glycoeffect": [], "start_pos": 1642, "end_pos": 1642, "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072054", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1642", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778803592", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778803592" }, { "id": "rs1778803592", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1778803592" } ], "glycoeffect": [], "start_pos": 1642, "end_pos": 1642, "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072055", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1642", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1293823599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1293823599" }, { "id": "rs1293823599", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1293823599" } ], "glycoeffect": [], "start_pos": 1643, "end_pos": 1643, "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072052", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1643", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1778802691", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1778802691" }, { "id": "rs1778802691", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1778802691" } ], "glycoeffect": [], "start_pos": 1644, "end_pos": 1644, "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072049", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1644", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs762859726", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762859726" }, { "id": "rs762859726", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762859726" }, { "id": "rs762859726", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762859726#frequency_tab" }, { "id": "rs762859726", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762859726" } ], "glycoeffect": [], "start_pos": 1644, "end_pos": 1644, "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072050", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1644", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs752427934", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752427934" }, { "id": "rs752427934", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752427934" }, { "id": "rs752427934", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752427934" } ], "glycoeffect": [], "start_pos": 1645, "end_pos": 1645, "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072047", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1645", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1647, "end_pos": 1647, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072040", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1647", "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": "rs1335605696", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1335605696" }, { "id": "rs1335605696", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1335605696" } ], "glycoeffect": [], "start_pos": 1649, "end_pos": 1649, "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072033", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1649", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770472122", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770472122" }, { "id": "rs770472122", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770472122" }, { "id": "rs770472122", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770472122" } ], "glycoeffect": [], "start_pos": 1650, "end_pos": 1650, "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072030", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1650", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776229083", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776229083" }, { "id": "rs776229083", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776229083" }, { "id": "rs776229083", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776229083" } ], "glycoeffect": [], "start_pos": 1650, "end_pos": 1650, "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072031", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1650", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1651, "end_pos": 1651, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072028", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1651", "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": "rs963344266", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs963344266" }, { "id": "rs963344266", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs963344266#frequency_tab" }, { "id": "rs963344266", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs963344266" } ], "glycoeffect": [], "start_pos": 1651, "end_pos": 1651, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072029", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1651", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201184519", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201184519" }, { "id": "rs201184519", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201184519" }, { "id": "rs201184519", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201184519" }, { "id": "rs201184519", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201184519" }, { "id": "rs201184519", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201184519" } ], "glycoeffect": [], "start_pos": 1653, "end_pos": 1653, "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072023", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1653", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] }, { "disease_id": "DOID:9620", "recommended_name": { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesicoureteral reflux", "description": "A ureteral disease characterized by backward flow of urine from the urinary bladder into the ureter." }, "synonyms": [ { "id": "DOID:9620", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9620", "name": "vesico-ureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "Vesicoureteral reflux", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "vesicoureteral reflux 1", "description": "" }, { "id": "MONDO:0008653", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008653", "name": "VUR", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "vesicoureteral reflux, X-linked", "description": "" }, { "id": "MONDO:0010755", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010755", "name": "VURX", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the ROBO2 gene." }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "ROBO2 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux (disease) caused by mutation in ROBO2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "vesicoureteral reflux type 2", "description": "" }, { "id": "MONDO:0012573", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012573", "name": "VUR2", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the SOX17 gene." }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "SOX17 vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux (disease) caused by mutation in SOX17", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "vesicoureteral reflux type 3", "description": "" }, { "id": "MONDO:0013356", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013356", "name": "VUR3", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "VUR4", "description": "" }, { "id": "MONDO:0013682", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013682", "name": "vesicoureteral reflux 4", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "VUR5", "description": "" }, { "id": "MONDO:0013683", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013683", "name": "vesicoureteral reflux 5", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "VUR6", "description": "" }, { "id": "MONDO:0013684", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013684", "name": "vesicoureteral reflux 6", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "VUR7", "description": "" }, { "id": "MONDO:0014161", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014161", "name": "vesicoureteral reflux 7", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "Any vesicoureteral reflux in which the cause of the disease is a mutation in the TNXB gene." }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "TNXB vesicoureteral reflux (disease)", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux (disease) caused by mutation in TNXB", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "vesicoureteral reflux type 8", "description": "" }, { "id": "MONDO:0014422", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014422", "name": "VUR8", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "luteal-phase-dependent periodic fever", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "menstrual cycle-dependent febrile episode", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle dependent", "description": "" }, { "id": "MONDO:0044660", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0044660", "name": "periodic fever, menstrual cycle-dependent", "description": "" }, { "id": "MIM:610878", "resource": "MIM", "url": "https://www.omim.org/entry/610878", "name": "Vesicoureteral reflux 2", "description": "Vesicoureteral reflux 2" }, { "id": "MIM:613674", "resource": "MIM", "url": "https://www.omim.org/entry/613674", "name": "Vesicoureteral reflux 3", "description": "Vesicoureteral reflux 3" }, { "id": "MIM:615963", "resource": "MIM", "url": "https://www.omim.org/entry/615963", "name": "Vesicoureteral reflux 8", "description": "Vesicoureteral reflux 8" }, { "id": "MIM:614674", "resource": "MIM", "url": "https://www.omim.org/entry/614674", "name": "Periodic fever, menstrual cycle-dependent", "description": "Periodic fever, menstrual cycle-dependent" } ], "unlinked_id_list": [], "evidence": [ { "id": "9620", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9620" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs772454700", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772454700" }, { "id": "rs772454700", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772454700" }, { "id": "rs772454700", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772454700#frequency_tab" }, { "id": "rs772454700", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772454700" } ], "glycoeffect": [], "start_pos": 1653, "end_pos": 1653, "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072022", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1653", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772454700", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772454700" }, { "id": "rs772454700", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772454700" }, { "id": "rs772454700", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772454700#frequency_tab" }, { "id": "rs772454700", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772454700" }, { "id": "rs772454700", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772454700" } ], "glycoeffect": [], "start_pos": 1653, "end_pos": 1653, "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072022", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1653", "disease": [ { "disease_id": "DOID:0080731", "recommended_name": { "id": "DOID:0080731", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080731", "name": "Ehlers-Danlos syndrome classic-like 1", "description": "An Ehlers-Danlos syndrome that is characterized by hyperextensible skin, hypermobile joints, and tissue fragility and that has_material_basis_in omozygous or heterozygous mutation in the tenascin-XB gene (TNXB) on chromosome 6p21." }, "synonyms": [ { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like type", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDS due to TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "EDSCLL", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "Ehlers-Danlos-like syndrome due to tenascin-X deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "TNX deficiency", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "clEDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like EDS", "description": "" }, { "id": "MONDO:0011670", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011670", "name": "classical-like Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:606408", "resource": "MIM", "url": "https://www.omim.org/entry/606408", "name": "Ehlers-Danlos syndrome, classic-like, 1", "description": "Ehlers-Danlos syndrome, classic-like, 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "606408", "database": "MIM", "url": "https://www.omim.org/entry/606408" }, { "id": "0080731", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080731" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs748623597", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748623597" }, { "id": "rs748623597", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748623597" }, { "id": "rs748623597", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748623597#frequency_tab" }, { "id": "rs748623597", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748623597" } ], "glycoeffect": [], "start_pos": 1654, "end_pos": 1654, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072020", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1654", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs779160751", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779160751" }, { "id": "rs779160751", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779160751" }, { "id": "rs779160751", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779160751#frequency_tab" }, { "id": "rs779160751", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779160751" }, { "id": "rs779160751", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs779160751" } ], "glycoeffect": [], "start_pos": 1654, "end_pos": 1654, "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072019", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1654", "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" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1655, "end_pos": 1655, "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072016", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1655", "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" ] }, { "evidence": [ { "id": "rs1051593704", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1051593704" }, { "id": "rs1051593704", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1051593704#frequency_tab" }, { "id": "rs1051593704", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1051593704" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1655, "end_pos": 1655, "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32072015", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1655", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" }, { "id": "rs749552054", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749552054" }, { "id": "rs749552054", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749552054" }, { "id": "rs749552054", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749552054" }, { "id": "rs749552054", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs749552054" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1658, "end_pos": 1658, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32072008", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S1658", "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": "rs779024434", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779024434" }, { "id": "rs779024434", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779024434" }, { "id": "rs779024434", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779024434" } ], "glycoeffect": [], "start_pos": 165, "end_pos": 165, "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tenascin xb (r. steet).", "chr_id": "6", "chr_pos": "32097359", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P165", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P22105", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22105" } ], "glycoeffect": [], "start_pos": 1661, "end_pos": 1661, "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tenascin xb (r. steet)).", "chr_id": "6", "chr_pos": "32071999", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1661", "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" ] } ] } }