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glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521385", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1027", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1281721856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1281721856" }, { "id": "rs1281721856", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1281721856#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1030, "end_pos": 1030, "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->K); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521395", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1030", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768477797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768477797" }, { "id": "rs768477797", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768477797" }, { "id": "rs768477797", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768477797" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1031, "end_pos": 1031, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521397", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1031", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs949580210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs949580210" }, { "id": "rs949580210", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs949580210" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1031, "end_pos": 1031, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521398", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1031", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2479055950", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2479055950" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1041, "end_pos": 1041, "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->P); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521427", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1041", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750510960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510960" }, { "id": "rs750510960", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510960" }, { "id": "rs750510960", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750510960" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1052, "end_pos": 1052, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521461", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1052", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P13611", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P13611" }, { "id": "rs377090663", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377090663" }, { "id": "rs377090663", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377090663" }, { "id": "rs377090663", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377090663#frequency_tab" }, { "id": "rs377090663", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377090663" }, { "id": "rs377090663", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs377090663" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1069, "end_pos": 1069, "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 2 out of 6 filters: num. of cancers (3); n-glyco-sequon-gain (DGS->NGS).", "chr_id": "5", "chr_pos": "83521511", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D1069", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. 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"resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": 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cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": 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"ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2135", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1262639975", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262639975" }, { "id": "rs1262639975", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262639975" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2144, "end_pos": 2144, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83539434", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs371992747", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371992747" }, { "id": "rs371992747", "database": "ExAC", "url": 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"evidence": [ { "id": "rs1357394432", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357394432" }, { "id": "rs1357394432", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357394432" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2530, "end_pos": 2530, "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->P); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540591", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2530", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746934260", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746934260" }, { "id": "rs1746934260", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1746934260" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2530, "end_pos": 2530, "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->Y); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540592", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2530", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1009437763", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009437763" }, { "id": "rs1009437763", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1009437763" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2540, "end_pos": 2540, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540622", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2540", "keywords": [ "ebi", "germline" 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"https://www.ensembl.org/id/rs2112447887" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2559, "end_pos": 2559, "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->R); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540679", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2559", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2479119933", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2479119933" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2571, "end_pos": 2571, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540715", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2571", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs149032014", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149032014" }, { "id": "rs149032014", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149032014" }, { "id": "rs149032014", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149032014" }, { "id": "rs149032014", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149032014#frequency_tab" }, { "id": "rs149032014", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149032014" }, { "id": "rs149032014", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149032014" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2572, "end_pos": 2572, "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 2 filters: o-glyco-site-loss (S->L); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540718", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2572", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1746940560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746940560" }, { "id": "rs1746940560", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1746940560#frequency_tab" }, { "id": "rs1746940560", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1746940560" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2583, "end_pos": 2583, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540750", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2583", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs780511968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780511968" }, { "id": "rs780511968", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780511968" }, { "id": "rs780511968", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780511968" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 2610, "end_pos": 2610, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (DES->NES); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540831", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D2610", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755439783", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755439783" }, { "id": "rs755439783", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755439783" }, { "id": "rs755439783", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755439783#frequency_tab" }, { "id": "rs755439783", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755439783" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 2615, "end_pos": 2615, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (DST->NST); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540846", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D2615", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201327923", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201327923" }, { "id": "rs201327923", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201327923" }, { "id": "rs201327923", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201327923" }, { "id": "rs201327923", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201327923#frequency_tab" }, { "id": "rs201327923", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201327923" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 2628, "end_pos": 2628, "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NLS->KLS); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540887", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N2628", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746950252", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746950252" }, { "id": "rs1746950252", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1746950252" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "start_pos": 2630, "end_pos": 2630, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NLS->NLF); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540892", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2630", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753104597", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753104597" }, { "id": "rs753104597", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753104597" }, { "id": "rs753104597", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753104597#frequency_tab" }, { "id": "rs753104597", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753104597" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 2645, "end_pos": 2645, "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (SYT->NYT); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540937", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2645", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1211231666", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1211231666" }, { "id": "rs1211231666", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1211231666" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 2652, "end_pos": 2652, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (DES->NES); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540957", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D2652", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs756823982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756823982" }, { "id": "rs756823982", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756823982" }, { "id": "rs756823982", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756823982#frequency_tab" }, { "id": "rs756823982", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756823982" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2656, "end_pos": 2656, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540969", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2656", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs150166604", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150166604" }, { "id": "rs150166604", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150166604" }, { "id": "rs150166604", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150166604#frequency_tab" }, { "id": "rs150166604", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150166604" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2656, "end_pos": 2656, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540970", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2656", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1402773257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402773257" }, { "id": "rs1402773257", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1402773257#frequency_tab" }, { "id": "rs1402773257", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402773257" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2661, "end_pos": 2661, "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->G); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83540984", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2661", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2112448662", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2112448662" }, { "id": "rs2112448662", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2112448662" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 2669, "end_pos": 2669, "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (HFT->NFT); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541008", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H2669", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746959024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746959024" }, { "id": "rs1746959024", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1746959024" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2671, "end_pos": 2671, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541014", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2671", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs61733390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61733390" }, { "id": "rs61733390", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61733390" }, { "id": "rs61733390", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61733390" }, { "id": "rs61733390", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61733390#frequency_tab" }, { "id": "rs61733390", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61733390" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2671, "end_pos": 2671, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541015", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00137363", "site_lbl": "T2671", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1434129544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1434129544" }, { "id": "rs1434129544", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1434129544#frequency_tab" }, { "id": "rs1434129544", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1434129544" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2691, "end_pos": 2691, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541075", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2691", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763286067", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763286067" }, { "id": "rs763286067", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763286067" }, { "id": "rs763286067", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763286067" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2699, "end_pos": 2699, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->F); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541099", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2699", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1197311115", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1197311115" }, { "id": "rs1197311115", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1197311115" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2701, "end_pos": 2701, "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->K); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541105", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2701", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1561258611", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1561258611" }, { "id": "rs1561258611", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1561258611" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2723, "end_pos": 2723, "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->N); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541171", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2723", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2112449172", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2112449172" }, { "id": "rs2112449172", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2112449172" }, { "id": "rs778883363", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778883363" }, { "id": "rs778883363", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778883363" }, { "id": "rs778883363", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778883363#frequency_tab" }, { "id": "rs778883363", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778883363" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2723, "end_pos": 2723, "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss 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"TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1369077171#frequency_tab" }, { "id": "rs1369077171", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369077171" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2760, "end_pos": 2760, "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->P); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541281", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2760", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1226021119", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226021119" }, { "id": "rs1226021119", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1226021119#frequency_tab" }, { "id": "rs1226021119", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1226021119" } ], 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[ "o-glyco-site-loss" ], "start_pos": 2977, "end_pos": 2977, "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->C); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541933", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2977", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1747014755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1747014755" }, { "id": "rs1747014755", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1747014755" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2978, "end_pos": 2978, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541936", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2978", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1201226006", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1201226006" }, { "id": "rs1201226006", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1201226006" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2981, "end_pos": 2981, "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->P); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541944", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2981", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2112450864", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2112450864" }, { "id": "rs2112450864", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2112450864" }, { "id": "rs2112450864", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2112450864" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 2983, "end_pos": 2983, "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83541951", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2983", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs756880346", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756880346" }, { "id": "rs756880346", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756880346" }, { "id": "rs756880346", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756880346#frequency_tab" }, { "id": "rs756880346", "database": "gnomAD", "url": 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"5", "chr_pos": "83542020", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S3006", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757872221", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757872221" }, { "id": "rs757872221", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757872221" }, { "id": "rs757872221", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757872221" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 3024, "end_pos": 3024, "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->Y); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83542074", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S3024", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs367904766", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367904766" }, { "id": "rs367904766", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367904766" }, { "id": "rs367904766", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs367904766#frequency_tab" }, { "id": "rs367904766", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367904766" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 3025, "end_pos": 3025, "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->M); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83542077", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T3025", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1265659118", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265659118" }, { 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type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83542089", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S3029", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753158938", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753158938" }, { "id": "rs753158938", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753158938" }, { "id": "rs753158938", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753158938" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 3045, "end_pos": 3045, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83542136", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T3045", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs73148633", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs73148633" }, { "id": "rs73148633", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs73148633" }, { "id": "rs73148633", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs73148633" }, { "id": "rs73148633", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs73148633#frequency_tab" }, { "id": "rs73148633", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs73148633" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 3045, "end_pos": 3045, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83542137", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T3045", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs73148633", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs73148633" }, { "id": "rs73148633", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs73148633" }, { "id": "rs73148633", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs73148633" }, { "id": "rs73148633", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs73148633#frequency_tab" }, { "id": "rs73148633", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs73148633" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 3045, "end_pos": 3045, "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->K); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83542137", "ref_nt": "A", "alt_nt": "null", 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"83542137", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T3045", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2479126690", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2479126690" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 3067, "end_pos": 3067, "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NET->SET); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83542203", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N3067", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1180337461", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1180337461" }, { "id": "rs1180337461", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1180337461" } ], "glycoeffect": [ 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"alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T3069", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs372945040", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372945040" }, { "id": "rs372945040", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372945040" }, { "id": "rs372945040", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372945040#frequency_tab" }, { "id": "rs372945040", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372945040" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 3097, "end_pos": 3097, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (NPC->NAC); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83545560", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P3097", "keywords": [ 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mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519804", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T500", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1390722075", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1390722075" }, { "id": "rs1390722075", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1390722075#frequency_tab" }, { "id": "rs1390722075", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1390722075" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 500, "end_pos": 500, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519805", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T500", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1390722075", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1390722075" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 500, "end_pos": 500, "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->R); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519805", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T500", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746011633", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746011633" }, { "id": "rs1746011633", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1746011633#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 516, "end_pos": 516, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519853", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T516", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs756803099", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756803099" }, { "id": "rs756803099", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756803099" }, { "id": "rs756803099", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756803099" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 516, "end_pos": 516, "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->P); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519852", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T516", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746018229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746018229" }, { "id": "rs1746018229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1746018229" }, { "id": "rs1746018229", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1746018229" }, { "id": "rs1561243463", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1561243463" }, { "id": "rs1561243463", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1561243463" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 522, "end_pos": 522, "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520015", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T522", "keywords": [ "ebi", "somatic", "germline" ] }, { "evidence": [ { "id": "rs1386848087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386848087" }, { "id": "rs1386848087", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386848087" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 538, "end_pos": 538, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (TVS->NVS); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519919", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T538", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs536252273", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536252273" }, { "id": "rs536252273", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536252273" }, { "id": "rs536252273", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs536252273" }, { "id": "rs536252273", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs536252273#frequency_tab" }, { "id": "rs536252273", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs536252273" }, { "id": "rs536252273", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs536252273" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 544, "end_pos": 544, "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520081", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T544", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1482034579", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482034579" }, { "id": "rs1482034579", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1482034579#frequency_tab" }, { "id": "rs1482034579", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1482034579" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 551, "end_pos": 551, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519958", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T551", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746016534", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746016534" }, { "id": "rs1746016534", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1746016534#frequency_tab" }, { "id": "rs1746016534", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1746016534" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 559, "end_pos": 559, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (DRT->NRT); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519981", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D559", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760401724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760401724" }, { "id": "rs760401724", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs760401724" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 563, "end_pos": 563, "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->R); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83519994", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T563", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1333450409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1333450409" }, { "id": "rs1333450409", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1333450409#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 569, "end_pos": 569, "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->N); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520012", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S569", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766131650", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766131650" }, { "id": "rs766131650", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766131650" }, { "id": "rs766131650", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766131650#frequency_tab" }, { "id": "rs766131650", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766131650" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 569, "end_pos": 569, "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (S->R); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520013", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S569", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746018229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746018229" }, { "id": "rs1746018229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1746018229" }, { "id": "rs1746018229", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1746018229" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 570, "end_pos": 570, "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520015", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T570", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1746018229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746018229" }, { "id": "rs1746018229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1746018229" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 570, "end_pos": 570, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->N); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520015", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T570", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1744933219", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1744933219" }, { "id": "rs1744933219", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1744933219#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 57, "end_pos": 57, "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NTS->HTS); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83490196", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N57", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2478963803", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2478963803" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 57, "end_pos": 57, "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NTS->TTS); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83490197", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N57", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746020406", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746020406" }, { "id": "rs1746020406", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1746020406" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 589, "end_pos": 589, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->N); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520072", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T589", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1580627339", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1580627339" }, { "id": "rs1580627339", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1580627339" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 589, "end_pos": 589, "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->P); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520071", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T589", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1395985141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395985141" }, { "id": "rs1395985141", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1395985141" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 590, "end_pos": 590, "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (IHT->NHT); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520075", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I590", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1367769624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367769624" }, { "id": "rs1367769624", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1367769624#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "start_pos": 59, "end_pos": 59, "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss 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"S59", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746024055", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746024055" }, { "id": "rs1746024055", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1746024055" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 615, "end_pos": 615, "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NGS->SGS); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520150", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N615", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs143729093", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143729093" }, { "id": "rs143729093", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143729093" }, { "id": "rs143729093", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143729093" }, { "id": "rs143729093", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143729093#frequency_tab" }, { "id": "rs143729093", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143729093" }, { "id": "rs143729093", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143729093" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 632, "end_pos": 632, "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 2 filters: o-glyco-site-loss (T->M); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520201", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T632", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs761622471", "database": "dbSNP", "url": 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mutation passed 2 filters: o-glyco-site-loss (T->R); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520516", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T737", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750786127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750786127" }, { "id": "rs750786127", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750786127" }, { "id": "rs750786127", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750786127" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 751, "end_pos": 751, "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520557", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": 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o-glyco-site-loss (T->A); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520911", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T869", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1261180767", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1261180767" }, { "id": "rs1261180767", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1261180767#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 887, "end_pos": 887, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: o-glyco-site-loss (T->I); glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83520966", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T887", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1261180767", "database": "dbSNP", "url": 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"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" ] }, { "evidence": [ { "id": "rs1746102396", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746102396" }, { "id": "rs1746102396", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1746102396#frequency_tab" } ], "glycoeffect": [], "start_pos": 1090, "end_pos": 1090, "sequence_org": "L", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521574", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1090", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs140933632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140933632" }, { "id": "rs140933632", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140933632" }, { "id": "rs140933632", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs140933632#frequency_tab" }, { "id": "rs140933632", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs140933632" } ], "glycoeffect": [], "start_pos": 1094, "end_pos": 1094, "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521586", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1094", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P13611", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P13611" } ], "glycoeffect": [], "start_pos": 1094, "end_pos": 1094, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "Q", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "5", "chr_pos": "83521587", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1094", "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": "rs140933632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140933632" }, { "id": "rs140933632", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140933632" }, { "id": "rs140933632", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs140933632#frequency_tab" }, { "id": "rs140933632", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs140933632" } ], "glycoeffect": [], "start_pos": 1094, "end_pos": 1094, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521586", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1094", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P13611", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P13611" } ], "glycoeffect": [], "start_pos": 1095, "end_pos": 1095, "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "A", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "5", "chr_pos": "83521590", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "V1095", "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": "P13611", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P13611" } ], "glycoeffect": [], "start_pos": 1096, "end_pos": 1096, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "5", "chr_pos": "83521593", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G1096", "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": "rs1746103334", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746103334" }, { "id": "rs1746103334", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1746103334" } ], "glycoeffect": [], "start_pos": 1096, "end_pos": 1096, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521592", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1096", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201077399", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201077399" }, { "id": "rs201077399", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201077399" }, { "id": "rs201077399", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201077399" }, { "id": "rs201077399", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201077399#frequency_tab" }, { "id": "rs201077399", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201077399" }, { "id": "rs201077399", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201077399" } ], "glycoeffect": [], "start_pos": 1096, "end_pos": 1096, "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521737", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1096", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs769770175", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769770175" }, { "id": "rs769770175", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs769770175" } ], "glycoeffect": [], "start_pos": 1097, "end_pos": 1097, "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521595", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1097", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P13611", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P13611" }, { "id": "rs1202478283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202478283" }, { "id": "rs1202478283", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1202478283" }, { "id": "rs1202478283", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1202478283" } ], "glycoeffect": [], "start_pos": 1098, "end_pos": 1098, "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "I", "sequence_mut": "S", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "5", "chr_pos": "83521599", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "I1098", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs2479057219", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2479057219" } ], "glycoeffect": [], "start_pos": 1098, "end_pos": 1098, "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521598", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1098", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746103934", "database": 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"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": "rs1317762793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1317762793" }, { "id": "rs1317762793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1317762793" } ], "glycoeffect": [], "start_pos": 1136, "end_pos": 1136, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521713", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1746109314", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1746109314" }, { "id": "rs1746109314", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1746109314" } ], "glycoeffect": [], "start_pos": 1136, "end_pos": 1136, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521712", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750662669", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750662669" }, { "id": "rs750662669", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750662669" }, { "id": "rs750662669", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750662669" } ], "glycoeffect": [], "start_pos": 1137, "end_pos": 1137, "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521717", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1137", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767840246", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767840246" }, { "id": "rs767840246", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767840246" }, { "id": "rs767840246", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767840246#frequency_tab" }, { "id": "rs767840246", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767840246" } ], "glycoeffect": [], "start_pos": 1137, "end_pos": 1137, "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521715", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E1137", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1467314422", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467314422" }, { "id": "rs1467314422", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467314422#frequency_tab" }, { "id": "rs1467314422", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467314422" } ], "glycoeffect": [], "start_pos": 1138, "end_pos": 1138, "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521718", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1138", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1467314422", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467314422" }, { "id": "rs1467314422", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467314422#frequency_tab" }, { "id": "rs1467314422", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467314422" } ], "glycoeffect": [], "start_pos": 1138, "end_pos": 1138, "sequence_org": "Q", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/c-type/proteoglycan.", "chr_id": "5", "chr_pos": "83521718", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q1138", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P13611", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P13611" } ], "glycoeffect": [], "start_pos": 1139, "end_pos": 1139, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "*", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "5", "chr_pos": "83521721", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K1139", "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": "P13611", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P13611" } ], "glycoeffect": [], "start_pos": 1139, "end_pos": 1139, "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "5", "chr_pos": "83521723", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K1139", "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": 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